That Sinking Feeling


Author's note: Okay, I want you all to know that I am suffering for my art. My laptop, which I use for all my typing, has lost its letter "A" key. I still have the key, but it will not go back on. Having seen how it was attached, I do not feel in any way qualified to reattach it even if it were not broken. So…whining completed, here is my next story. It has been hovering in the back of my mind for quite some time now, and I finally had to do it. My new beta, bless her, is even as you read this hacking her way through my other really big story (probably with a machete), and I thought I would post this as a fill in while I waited. (Yes, this is a small story for me) This takes place in the third season mainly because I wanted to use Carson…DO NOT get me started on THAT decision by the producers. Anyway, this contains the usual Shep whump, but that doesn't mean that I don't love him. Gimmie!

Chapter 1-

Lt Colonel John Sheppard stifled a cough as he sauntered down the corridor toward the control room of his base. Even after three years that phrase, 'his base', still caused a little thrill in his guts. He hadn't planned to be military commander of anything, much less the lost, and then found, city of Atlantis. Of course he hadn't had any clue that Atlantis wasn't just a myth, instead of being an actual city, an actual FLYING city. What more could an Air Force zoomie want? He had lived to fly, and now he lived in a flying city.

With a quick look around to make sure he was alone he pulled out a tissue and blew his stuffy nose. He knew that he probably wasn't fooling anyone, but it made him feel better to pretend that he simply didn't have what Carson was calling the Athosian flu. It wasn't like he was the only one suffering anyway. About half of the base was moaning and groaning and the other half was avoiding them like they had the plague. Of course in a closed environment it was pretty much impossible to avoid someone with the flu. He had gotten it from McKay who had gotten it from Teyla, who had gotten it from someone on the mainland who had gotten it from god knows where. "May that person be cursed" He thought.

The number of personnel involved including at least half of their own people had overwhelmed Carson and the rest of the medical section. It wasn't like they could do much besides treat the symptoms anyway, it was a virus, and there wasn't anything to do. It was generally keep warm, eat when you can, rest as much as possible, take something for the aches and to keep any fever down. There had been a few serious cases, the flu developing into pneumonia, but so far it usually kicked your ass for a week then you got better. Unfortunately, Sheppard was at the start of the process. That meant he had another week of this. Joy.

Of course he might be feeling somewhat better if he would simply admit he was sick and take to his bed, but he refused to give in. Anyway, it wasn't like they had room service here, if he took to his bed that meant someone had to bring him food and check in on him. Things were stretched thin enough as if was. The marines had been hit harder than the scientists. Evidently there was a value to closing oneself in a lab and not emerging for days on end. So, he persevered, and tried to pretend that all of his muscles didn't feel like they had been overworked. He had been forced to stop after only just over a mile this morning during his run, unable to get his breath and feeling like he had run a marathon. Ronon, evidently proof against the virus, had simply nodded to him and kept going as he walked back to the nearest transporter and went to take a very long, very hot shower, and two Tylenol, okay, maybe it was three.

Now, he was due in the meeting room to discuss some new addresses that they would be visiting when the teams were once more going through the gate. Carson had quickly put a stop to all gate travel, with the exception of absolutely necessary medical aid and food trades already arranged, and then only by people who had already had the virus and recovered. He understood why it had to be, but he almost resented not being able to go off world, even if he didn't really need to be dodging angry natives right now. He could always threaten to sneeze on them.

He strolled into the meeting room and took his usual seat. Elizabeth was already there, going over something with Chuck the gate tech. Teyla was also already seated, and he cast her a smile that she returned. She was still looking a little rocky from the effects of the flu, but since even her bad looked good, she seemed to be nearly back to normal. It wasn't fair. Someone, probably Teyla, had put a cup of hot coffee in front of his seat, and he grabbed it thankfully. His throat was dry and scratchy, and it hurt to swallow. The hot liquid felt good going down. He hadn't mentioned that little symptom when Carson had cornered him in the mess hall that morning as he had poked at a bowl of oatmeal with no interest. He hoped it would just go away soon, but the dry cough was making it hard to hide.

McKay wondered into the room with a huge mug of coffee, looking only slightly better than death warmed over. He had lost a few pounds, something he seemed to be trying to remedy at breakfast this morning, and he was still a little pale. His acerbic wit had never faltered however, and he was back to harassing his scientists full time now in person instead of just by email and instant messaging. There was the barest possibility that the strangely coincidental crash of both the email and messenger servers might have had something to do with Rodney's recovery from what he had assured everyone was his deathbed. He sat down next to Sheppard and studied him with a jaundiced eye as he sipped at his bucket 'o coffee.

"Well you look like five miles of bad road." He observed with a smirk. He didn't wish anyone ill, but if he had to suffer through it, he didn't see why Sheppard should get off easy. He scowled slightly as Ronon Dex slipped into the room and sat down near Teyla. Ronon's continued resistance to the virus bugged the hell out of the scientist simply because he didn't see why the man mountain should be spared when others had been forced to endure.

"Since you're the one that ran me down on that road McKay, I would say you would know. Have I thanked you for this? I'll have to remember you at Christmas. I think I can get the cooks to make lemon meringue pies for the holiday." Sheppard said, not above taunting his friend with his allergies.

"Yes by all means let us taunt a man with his sensitivities. We wouldn't want to be adult about this, would we? You don't know you got it from me anyway." He sank back in his chair, his eyes never leaving Sheppard. Rodney was concerned about the colonel. He was looking very pale, and his voice didn't sound quite right.

"Well let's see McKay. Who was acting as your personal body slave for three days when you wouldn't do anything more strenuous then type poison pen letters to the guys in Chemistry?" Sheppard asked in his new husky voice. Definitely something wrong there. The colonel cleared his throat when he finished speaking and took a drink of his coffee.

"They were being more idiotic than normal, and I did what I could to rein them in so that we all didn't die in a puff of greenish nasty smelling smoke. Anyway, I was prostrate with a fever and weakened body. Someone had to take care of things, you were just…available." He knew that Sheppard could have found almost anyone else to take care of McKay when he had been stuck in bed for the last part of his illness. He had appreciated all the time that the colonel had spent with him, even going so far as to roll out his sleeping bag on the floor so that if McKay had needed anything in the night someone was at hand. It was during all that time that he had probably picked up the virus. Rodney could never tell him how much he had appreciated his help and presence. Their friendship just wasn't like that.

"Your fever never went over a hundred, Rodney." came the soft Scottish burr over McKay's shoulder as Carson Beckett slipped into the chair on the other side. He leaned forward and looked at Sheppard. "You will report to the infirmary when this meeting is over, colonel. Your condition has obviously degraded since I saw you earlier. This is progressing a bit faster than the norm with you, and I want to make sure that we don't end up with another case of pneumonia on our hands." Sheppard was about to protest when he felt another cough trying to force its way out, and it was all he could do to keep it in. If he opened his mouth he would certainly give it away. There was still hope, he should be able to make it through the exam without being restricted to quarters, but he had to put on as good a front as possible. He settled for slumping down in his chair with a slight pout. At the head of the table Elizabeth had finished her talk with Chuck and he left the room as she called the meeting to order.

Looking around the table, Elizabeth Weir could only marvel at the people she had been gifted with for this expedition. She herself felt crappy, and intended to go back to bed as soon as the meeting was over. She knew that Teyla and McKay had just overcome the virus, but they were here, and they had performed their duties even while sick. Carson Beckett was looking like he hadn't slept in days, and she was pretty sure he hadn't to speak of. His division, with his firm guidance, was dealing with the epidemic smoothly and with complete professionalism, even when faced with the whining of large numbers of scientists and marines, neither of who made good patients. Ronon Dex, an island of immunity in the middle of it all, had stepped up to fill in for several of the off world team members. It was his presence on the one remaining off world team that had made the continuing missions possible, as the other members were scientists or untrained marines who had never gone off world. He was all the security anyone could want it seemed. Her eyes went last to her Military commander. John Sheppard had been everywhere in the last two weeks. He had filled in on guard duty, had worked one rotation in the kitchen-he would have worked more probably, but the protest over his burnt offering of toast had been almost unanimous- she knew he had been spending time with Rodney, even going as far as to bunk in his quarters when the scientist had refused to get out of bed. He had also made sure to drop in on as many of his marines who were on bed rest as he could manage each day. It had come to no surprise when she had seen him the night before, trying to stretch the ache out of muscles that wouldn't stop hurting and looking a little pale. He was even more so now, and obviously was trying to pretend that he didn't feel just as bad as she did. What a wonderful group of people she had. She keyed up the first possible gate address on her tablet.

"P3V-1786. What do we have on it?" Best to get this over with quickly.

Chapter 2-

They had worked through more than half of the possible planets, finding four that would definitely be visited, three possibles, and two definite no-goes, before Elizabeth decided that pausing for lunch would be a good idea. She was pretty sure that John had gone to sleep with his eyes open almost an hour earlier. He hadn't so much as twitched through all of the arguing and discussion that had gone on. She started to break up the newest 'discussion' between Rodney and Ronon about a planet that Ronon said was completely dead and suggest a break, and possibly a visit to the infirmary for John when an alarm that they had not heard before began sounding.

Sheppard went from a seemingly boneless sprawl in his chair to rushing from the room almost in an instant. The rest, except for Ronon who was on Sheppard's heels, sat for a moment in confusion and then almost as one they followed the two men. When they reached the control room Sheppard was leaning over the tech's shoulder looking at the screen. As the rest of them came up the tech was speaking.

'I don't know Colonel. It's not long-range sensors. It seems to be something inside Atlantis." He said in frustration. He then grunted as McKay forced him out of the chair, toppling him on to the floor. The scientist sat down and began typing furiously. When Elizabeth started to question him he held up a finger and went back to typing. He touched his radio and soon was deep in geek speak with Radek Zalenka who was no doubt doing a similar dance on his own keyboard. After almost five minutes the rest of the senior staff was beginning to shift nervously as McKay's pace did not slacken, nor did the alarm go off. Finally McKay stopped typing and listened to something Zalenka was saying. The he bent forward over the machine again.

"What!" He barked. "Who the hell…No I don't supposed it really matters at this point, but wouldn't it be nice to know how they did it so it doesn't happen again, providing of course that there is anyone here to do it again. Where did you say you found it?" He typed furiously then bent over the screen, reading swiftly. His face paled. "Are you reading this Radek?" He asked quietly. At the tone Sheppard shifted nervously. McKay was never quiet, except when it was really bad. McKay looked up from the screen and around at them all.

"Go away. It's going to take some time to determine just how much trouble we are in. I'll let you know as soon as we have an answer. You might want to consider getting ready for an evacuation however." With that dire warning he turned and resumed reading, murmuring to Zalenka as he scrolled. The alarm cut off without warning, leaving them with a silence that was all the more startling for its contrast. Sheppard was the first to move, his hand moving up to his own radio.

"Attention all military personnel, we are looking at a possible bug out situation. Evacuation plan Delta Chi is now in effect. All officers will report to the wardroom immediately for assignments." He started toward the corridor, but Elizabeth called his name. He spun around.

"John we don't even know what's happening yet. You can get everyone moving on an evacuation with no information." She said. She didn't want to think about having to leave the city. They had fought too long and too hard, had lost too many, to give it up easily. She would not have thought John would be giving up without a fight either. She followed his eyes to where McKay was hunched over the computer. The man's whole body language screamed defeat, even as he was obviously searching for victory. Sheppard's eyes met hers. She could see the same anger, fear, and frustration there that she felt in herself, but there was also determination.

"We have too many things to do Elizabeth. If we do have to evac to the Alpha site we HAVE to have weapons, food, and security through first. The Daedalus can reroute and bring in what supplies they have there, but they can't arm us or house us. Even if we have to unpack it two hours from now, we have to be ready, worse comes to worse." He said simply, and she knew he was right. She nodded, and he left the control room, Ronon on his heels, reaching for his radio again. Carson moved to follow.

"If we have to leave I'll have to have a large facility to house those that are sick and recovering from this miserable flu. I have seventy-five people on bed rest now that will have to be somewhere they can be looked after and kept warm. I'll also have to get my people packing the medical supplies. We won't be able to count on the Daedalus having sufficient resources. We better get started. Like the Colonel said, we can always unpack." He was gone too, reaching for his radio as he went. Elizabeth took a deep breath, and knew she had to act as well. With a glance at McKay whose posture had not improved, she reached for her own radio and clicked on the general channel. She hoped she could find the right words.

An hour later a type of controlled chaos had taken over the city. People were moving everywhere. There were already crates and boxes beginning to stack up in the gate room and the corridors leading into it. Major Lorne, newly up from his sick bed, and looking like it, was acting as traffic coordinator for the increasing piles. He was prioritizing the listing and placement for what would go through to the Alpha site. She had not seen Sheppard since he had left, but she had heard him on the radio, almost constantly, moving through he city and coordinating the efforts of his men. She was reading over her own checklist when Rodney sat back from the computer and looked around at the chaos, as if he hadn't noticed what was going on until then. He probably hadn't. He looked around until he spotted her and rose to join her.

"Rodney, I hope that you are going to tell me that this was all a false alarm and we can all start unpacking now." She said hopefully, but she had only to look at him to know that he was not going to say any such thing. At his grim look she called Sheppard and Beckett, along with Teyla and the other department heads into the conference room. Minutes later they were almost all gathered. It was a silent and worried group that looked to where McKay and Zalenka were now huddled over a shared laptop. "Rodney?" she prompted when it looked as if the two were going to fall back into what Sheppard called the geek-speak mode. She saw John slip into the room, Ronon a tall shadow at his elbow, just before Rodney looked up and started to talk.

"Well the good news is that Atlantis is not going to blow up, be taken over by nanites, or loose power and leave us at the mercy of the wraith." He started. There was a sigh of relief that went away as he kept talking. "However, the bad news is…well pretty dismal. Somehow, we still haven't found out exactly how, someone has triggered the Atlantis computer system into a maintenance mode. Right now the system is busy cataloging all information that is stored ANYWHERE on any storage device in this city. That in itself is not a bad thing, however it is just the first step in a process that is…" He stopped and sighed. "The bottom line is that in about ten hours the city is going to shut down all non- essential systems, it is going to then turn on the shield, and it is going to sink itself back to the position where we found it, actually maybe even deeper. It is then going to put itself into a diagnostic mode and essentially defragment the entire system. Once again, not essentially a bad thing, but the Atlantis systems are very large and very complicated, and after ten thousand years probably has a lot of errors that would benefit from the defrag. But, non-essential systems include water, lights, sewer, heating, and here's the biggie, the stargate. We won't be able to stay while the process is going on."

"Why can't we just turn off the process, Rodney?" Elizabeth asked, knowing McKay would have tried, but needing to ask. She could see the sarcastic answer rising to McKay's lips, but he manfully forced it down, which gave her a very bad feeling.

"We have tried that." He managed civilly. "However once the program is started it cannot be stopped. Even rebooting the system will only restart the process. It is going to do it, and there is nothing we can do about it."

"We have the naquada generators, could we not power the lights, heating, and other minor systems with those?" This came from one of the department heads. McKay was shaking his head before he finished the question.

"It's not a question of where the power is coming from. The computer is simply shutting down everything so that the defragmentation is complete. It is going to be cold and dark."

"How long, Rodney?" the question came from Sheppard near the door. Blue eyes sought him out. Elizabeth knew how much it hurt Rodney to admit there was nothing he could do about a problem, and she knew that Sheppard knew too. He would keep it concise and to the point, not allowing any emotion to build.

"Ninety days." The room erupted into voices. She herself reeled at the thought of 3 months at the Alpha site, without the protection of Atlantis's shields or weapons. McKay was trying to speak, and a piercing whistle cut through the noise. Sheppard threw a thankful look at Ronon before he asked the next question in to the silence.

"Why so long?"

"The database itself is…I can't even compare it to anything on earth. It is huge. We've barely accessed a percent. Add to that all the control systems for the entire city, and that is the estimate we have come up with for how long it is going to take for the entire process to complete. Once it is done there appears to be a setting that will return the city to the state it was in when the process was begun, so it will resurface and we'll be able to return."

"Why would they put a program like this into place. If it effectively shut down the city how could it be used?" Another department head asked. Zalenka picked up that question.

"I believe that the program was created shortly before the ancients abandoned the city. I think that since they knew the city was going to sleep, that they took advantage of that to do the maintenance. The program was probably only meant to be used that one time, but it was there, waiting for just the right command to start never the less." There was more discussion. Finally Ronon whistled again, and Weir stood up. It seems she had no choice.

"Very well. We now know what we are facing. We cannot simply stay here and ride out the time. If it had been only a week or possibly two, a small contingent may have been able to survive it. We know that with the ZPM the shield will hold, and Atlantis will be safe, but it will not be hospitable. Nor will we be able to use the stargate, or have the Daedalus beam in supplies. This being the case we will have to evacuate to the Alpha site. I know that Colonel Sheppard and his people and the medical section have already begun preparing, as have the rest of you to some degree. We need to emphasize that we WILL be returning here when the process is completed. Only essential items should be packed. We will begin dialing the Alpha site immediately, and the military will begin moving in supplies and personnel. You each have a copy of the evacuation protocols. We have ten hours. Let's use it wisely." Most of the department heads left at that point, leaving the senior staff and Zalenka. Sheppard sank down in a chair and laid his head on the table. Beckett reached over and laid a hand on the colonel's forehead. When it was not instantly slapped away, the others shared a worried glance.

"Lad, I know that we don't have the time, but you need to come down and let me get you some antipyretics and some liquids. If you collapse you won't be doing anyone any good. I can have you out in an hour, and you can use your radio while the IV is dripping, otherwise we'll be carrying you through on a stretcher. I can guarantee it." There was a deep sigh, followed by a dry cough from the arms where the dark head was pillowed. Sheppard slumped back in his seat, a resigned look on his face.

"Okay Carson, but in a few minutes, okay. We have a few things to work out."

"I know. I'll be waiting. Don't make me come looking for you." With that last stern warning, and a look at Ronon that Sheppard did not see, he left. The remaining people waited as McKay and Zalenka finished up and the Czech scientist scurried off. They sat in silence, each aware of the passage of precious time.

"We need to leave a contingent on the mainland. Once the city rises again we need to be here to make sure no one else stakes a claim, and while I trust McKay and Zalenka, we've seen enough strange things go on here that I would rather we were ready to retake her as soon as she rises, whenever that is. Since I have the strongest gene I think I should be one of the people here. Lorne can handle the security on the Alpha site, and the Daedalus is only two and a half days away if we need something. I'm sure Teyla's people can leave us a couple of the shelters, and we can take supplies and one of the jumpers. I figure me, Ronon, a unit of Marines, maybe one of Rodney's scientists. Volunteers only. We shouldn't have to worry about the wraith at least. A small group like that wouldn't even be a snack for a hive ship, not that they should be looking."

"Why just 'one of my scientists', why can't I stay?" McKay demanded. If Sheppard was staying he saw no reason he shouldn't stay too, not that he wanted to, but he didn't want to be told he couldn't. As soon as he started speaking the dark head was shaking however.

"You'll be needed on the Alpha site, McKay. Since we're using the Ancient research facility as a base they are going to need someone who knows the systems. If there is an attack they'll need the shield. You figured it out once, that makes you the best man for the job. Ask if one of your lab monkeys want a three-week vacation from you. You'll be beating off volunteers with a stick once they figure out that the facility is not even a tenth the size of Atlantis. Most of them would volunteer to swim to the mainland rather than be stuck in an enclosed space with you." McKay scowled at him, but did not argue. It was perhaps an indication of his sickness that Sheppard did not notice the scheming light in the blue eyes.

"I notice that you did not include me, Colonel, in your contingent to stay. May I ask why?" this was from Teyla. She did not sound angry, but Sheppard still squirmed nervously in his chair. He had gotten good at reading Teyla's subtext over the years.

"They're going to need food and supplies why they are there, and you're the best trader we got. All your people are going along too, and I know you don't like to be out of touch that long. It just makes sense that you're there to support Elizabeth." When I won't be, was the unspokenpart of the speech that Teyla heard. She didn't like it, her team was being split up, but she could see the logic of the plan. She nodded once in agreement, and saw the gratitude in the colonel's dark eyes.

"I don't know John. The wraith could still come, and while as you say there won't be many of you, they could still attack. What then?" Elizabeth said. She knew he was right, but she had come to depend on him so much, she could not imagine three months without his council.

"We can get in the puddle jumper. If all else fails it's four days to the nearest stargate. If the Daedalus is nearby we can meet them somewhere. But I don't think that'll be a problem. We'll just be sitting around, hunting the wily squirrel-thing and letting Ronon beat us up. Like I said, the Daedalus is two days plus away from the Alpha site. We can change out the team as we go along if we have to." He had obviously thought this out, in his usual tactical way. It was one of the reasons she valued him so. She stared down at the table for a moment.

"You need to add a medical presence in the group." She held up a hand as he started to protest. "Not negotiable, colonel. You have the flu now, and there is no telling what might come up. If you have an injury four days in a puddle jumper is not going to cut it. Also, you should have another pilot in the group, in case something should happen."

"Already thought of that last part." Sheppard muttered. He drew a circle on the arm of his chair with his finger, not looking at her. "I'll talk to Beckett, have him ask for a volunteer. He's not going to like it."

"No, I don't imagine he will. But I'm sure that you can talk him into it. I have faith in you, John."

"Gee thanks." The colonel said and then levered himself up. "Guess I'll go see him now, before he comes looking." He started for the door. Without turning he spoke. "Coming, Chewie? Beckett will want to know that you've been keeping an eye on me." With that he was out the door. Ronon gave a shrug and a small smile. Trust Sheppard to see what others might miss. He followed the colonel out the door. He had made Sheppard one of his family and that meant that when he needed to be looked after Ronon would be there, whether Sheppard liked it or not.

Chapter 3-

Two hours later Ronon was following Sheppard again. The colonel had been in the infirmary until five minutes previously, and had left after a rather heated argument with the doctor. Sheppard had allowed the IV and some medications, but had threatened mayhem if any sedatives were used. Hence the colonel had spent the entire time, twice what Beckett had said, which Sheppard pointed out repeatedly, on his radio and talking with one person after the other, moving from clipboard to clipboard. It wasn't until he was back on his feet and ready to leave that Sheppard had brought up the plan for staying behind on the mainland. Beckett had indeed not been pleased to hear that Sheppard would not be joining the rest of them at the Alpha site. He had pointed out that the colonel was running a fever, had just had to have an IV to support his flagging system. He had used some words in a language that Ronon didn't recognize, and had suggested that Sheppard needed a psych evaluation. That wasn't new. After more arguing the doctor had finally caved, and asked for volunteers from his crew. One of the doctors had volunteered, and that was that. Sheppard had smiled that satisfied smile of his; pissing off Beckett all the more, and they had left hastily. Now they were headed toward the gate room and a quick trip to the Alpha site for an evaluation of the current status of the evacuation.

Sheppard was in full field kit, P-90 and all, and of course Ronon was always armed. He had simply thrown on his coat and was ready to go. He wasn't going to let Sheppard out of his sight. The colonel was pale, except for two swatches of color on his cheeks caused by the fever, but he seemed to be running on sheer determination, and Ronon had cause to know just how far that would take the man. As Sheppard had pointed out to Beckett, he would have plenty of time to rest once the city sank.

They went through the gate and took a quick tour of the Alpha facility. SGA-1 had found the site three months ago. It was a relatively large facility, one that had evidently been dedicated to shield technology. It didn't have a ZPM, but whatever energy source it did have, Ronon hadn't understood what McKay was talking about when he explained it, was more than enough to power the shield that covered it. McKay had theorized that it would withstand a wraith attack for an indefinite period. Of course your food would run out after a while, but that shouldn't be a problem. The wraith had culled everyone from the plant in the last big culling. They had no reason to return. But if they did, the Lanteans would be ready.

Sheppard seemed satisfied with what he saw. He talked with Lorne who had already set up a command center for almost an hour, going over plans and contingencies. Lorne hadn't been happy about Sheppard's plan, but he had been more circumspect in his objections. He tried to talk Sheppard into letting him go in his place, but was rebuffed swiftly. Then he tried to get him to take a larger group of marines along, but Sheppard pointed out that they could only get so many people in the puddle jumper in case of a problem. Lorne had conceded with good grace, and had asked for and gotten more volunteers than he needed. Ronon had noted with some amusement that Lorne had picked out the best of the best to send along, men that Ronon had fought and found adequate, if not up to his own standards. Sheppard had noted the selection too, but aside from a pointed look at his second, had not protested. One of the men was a pilot. They traveled back to Atlantis where people were beginning to gather in the gate room for departure. Most of the heavy moving had been done, and now it was mostly just personal luggage. Ronon didn't understand these people with three and four duffle bags. He had his stuff all in one small bag. It was only three months, how much did you need?

Sheppard surveyed the crowd, noting the military personnel mixed in with approval. An escort would go with each group of scientists until everyone was through. The last group out the gate would be security. By now the first jumper load of stuff should have been ferried over to the mainland. The marines, Ronon, the doctor, whichever scientist McKay had managed to browbeat into it, and the last of the supplies would go over in the next load. Whoever was flying would come back and then go with the security team. Then, right before she sank, Sheppard would be the last one to leave. He was planning on doing that alone, though he hadn't quite figured out how to get his extra large nanny to let him be. He hoped a direct order would do it, as he didn't think the marines were going to be up to keeping the Satedan in the jumper if he didn't want to be there. He had to find out what Beckett was bribing him with. As it turned out Ronon seemed to understand his desire, and went quietly

He met with Elizabeth one last time, and went over the final checklists. Everything seemed to be good. McKay and Zalenka had reported that the nonessential systems were starting to shut down, and that they figured that there was just under an hour and a half to go. Sheppard watched as Elizabeth took a look around her office and with a sigh picked up her backpack, the same one she had carried here three years before. He patted her arm.

"You'll be back in no time. Think of it as summer vacation in the mountains" The Alpha site was partially buried in the side of a mountain, and it was summer there now. "No more classes, no more books, no more teachers' dirty looks." He sing-songed. She smiled at him even though he could see the tears in her eyes she was trying hard to not let fall,

"Some of us liked being in school, and hated summer vacation. All we ever got was mosquito bites, sun burns, and our knees skinned up." She said teasingly.

"That was the fun part!" He said with a grin. She leaned forward and gave him an awkward hug. As always he didn't quite know what to do with his arms, but she still was somewhat happier when she drew back.

"Take care, John. We'll be able to relay messages through the Daedalus once we get established. I expect you to check in regularly. Oh, I also decided that you needed a second puddlejumper. They've left jumper one for you, and have taken number two. We'll have four others, and that's all we can really fit in the hanger there at the facility. Any others would have to be left outside, so I think this will be for the best. It never hurts to have a back up, isn't that what you're always telling me?" He couldn't argue with her there, so he gave in gracefully. Maybe that meant he could do a little exploring since there would be an extra jumper to leave behind in case of emergency. He might even be able to smuggle his surfboard on board since he was going to be alone, and should not be overloaded.

He escorted her down to the gate room floor, and she gathered her flock. She gave a little speech about how they were only going for a while, and how it would all be here when they got back. She managed to put enough confidence into it that everyone was looking a good deal better by the time she was done. He smiled as he remembered her speech on Earth three years before. The woman had a knack for inspiring.

The wormhole engaged again and the people began moving through. As each passed into the event horizon they were checked off a list. They would check in on the other side, and before the wormhole was shut down for the final time they would cross check. No one would be left behind. It was slow but steady work, but eventually only a few people remained. There was one science team in the labs monitoring the computers, Sheppard was surprised that McKay wasn't one of them, but he supposed that the scientist was busy getting the new facility up and running and the last of medical was pulling out with the last of the equipment. Sheppard called them all and told them to get a move on, and they were due in five minutes. He looked around, mentally tallying the marines, and seeing that everyone was accounted for. His radio going off interrupted his plan to run down to his quarters and grab his board to move it to the hanger. One of the scientists, a guy he hadn't met asked him to come to one of he labs, saying he had found something unexpected. He ran to the nearest transporter, worse case scenarios going through his head. He ran to the lab and thought the door open almost as soon as he was in sight of it. The scientist was standing over a computer screen, looking at something. Sheppard walked toward him.

"What did you find Dr…. uh…was it Margraves?" He asked. His focus was on the screen, not the man, so when the doctor turned around and was holding a wraith stunner, he didn't have any time to react before the blue light slammed into him and darkness closed around him.

Chapter 4-

Rodney McKay was very pleased with himself. He looked around the small hut that some Athosian had formally called home, and which was now his for the next 90 days. Well, his and Sheppard's. He supposed if he had to share with someone, it might as well be the colonel. After all they usually shared tents and huts when they were off world, and they could get along with each other. That was more than he could say for Ronon, or any of the marines, and who knew about that doctor. All those chicken entrails and incense would have been hell on his sinuses. He had managed, thorough a carefully planned campaign of pushiness and intimidation, to have his orthopedic mattress brought to the mainland in the first load of goods. He wasn't going to break his back lying on a pile of skins, or on one of those dreadful things the military called a cot for 3 months. Yes, it was on the floor, on top of a clean tarp, but still it was going to be the most comfortable bed in the place. He had also figured out how to use some of the crates holding MREs, just by chance the kind he liked best, to make a passable desk and chair. He had three laptops, a solar power station, and a communications base station set up. Of course there wasn't much room for anything else but Sheppard's cot, but how much room did the man need anyway? He only had one duffle bag of stuff, which was already sitting on the cot along with his sleeping bag. McKay couldn't wait to see his face. Consign him to the Alpha site would he?

Yes, things might have been slightly more…comfortable there, though he wasn't sure he could have pulled off the mattress coup. But he had found he didn't want to be there. Two of his three teammates were going to be here. Teyla would probably spend most of her time off world, trading, and he would have been…lonely. He didn't like to admit, even to himself, how much he had come to count on the daily interaction he had with his team. The meals, the meetings, the snarking, the movies, the simple acknowledgement when passing in the corridors, he was not ready to give that up. If that meant that he had to spend three months playing Boy Scout, then so be it. It wasn't as if he couldn't take a break and go back with the Daedalus sometime. They weren't completely cut off. Also, he was as reluctant to leave the city as Sheppard was. It was their city, his city, and when it rose again he intended to be there waiting for it. There were so many more mysteries that were left to uncover there, and he was the one to do the uncovering.

One of the laptops started beeping. He moved quickly to it, and flipped up the screen. It showed a countdown. As he watched the number slowly counted off until there was a zero on the screen. He flipped up another laptop, and hit a few buttons. He scanned quickly through the information that scrolled across the screen, and then sat down with a sigh. It was done. The city had sunk. He heard a sound at the doorway, and turned to see Ronon staring at him. He cast him a tired smile.

"Well, Conan, it just you, me, Sheppard, and a bunch of strangers against the wild now. Atlantis has sunk. There are no more data feeds being sent and the computer does not respond to any query. You might as well start teaching us how to skin a squirrel-thing and light a fire with no matches."

"It's not like we don't have ten years worth of MREs, McKay." The Satedan said with a small smile, eying one of the boxes that made up McKay's desk. He didn't read the English words well, but he was sure he recognized the word 'meatloaf'. McKay, seeing the predatory look, spread his arms protectively.

"Oh no, you keep your hands off my furniture. If you want to eat something start with Sheppard's cot, or his duffle. These are mine."

"If the city is sunk, shouldn't Sheppard be here already?" Ronon asked, scowling at the empty bed. He knew he shouldn't have agreed to come before Sheppard did.

"He's probably joyriding around in the jumper. You know how he gets when he can fly without anyone looking over his shoulder." Sheppard's team had been exposed to some of the most exciting rides ever to be had in a jumper courtesy of one hot shot pilot who sometimes just had to 'let loose'. Even inertial dampeners could only do so much, and then there were the times he shut those off for a more 'natural' feel; those times made even Ronon a little green. But even as McKay spoke he considered that Sheppard would have had to leave the city over 20 minutes before so that he could be sure to get off before the shield engaged. As much as the man loved to fly, he would have checked in one way or the other, to let them know what was going on. In fact, McKay had expected a blow-by-blow report of the sinking of Atlantis as told by that 'man in the air', John Sheppard. He reached for the radio.

"Puddle jumper one this is the mainland, come in." He broadcasted. He waited for a reply, but when none came he repeated the call. He waited again, exchanging looks with Ronon. He lifted the lid on the third of his laptops, the one that he had linked to the small satellites that orbited the planet. The ancients had been diligent in their placement, and he had complete coverage for the whole planet, as long as he had the access codes, which he did. He scanned from one to the next, muttering under his breath. When he didn't find what he wanted he punched in a new sequence of numbers and started scanning again. The frenetic activity slowed to a stop and he closed the laptop with a click. He simply sat there, staring at the closed computer for several seconds. Finally the silence was too much for Ronon.

"Well, where is he?" he asked. Something was wrong. The question was what could they do about it, and where exactly was Sheppard?

"I don't know." Came the surprising answer. It wasn't something he ever recalled McKay saying. "He's not anywhere on or around the planet, and he's not in the immediate vicinity of the planet." There was something in the flat delivery that made the hair on the back of Ronon's neck rise.

"Then where is he? Could he be further out, beyond the satellites?"

"No. No he's not." McKay said, still staring at the computer. Ronon let out a gust of air. This was like pulling a Derlian snake out of a hole.

"McKay. Where is Sheppard?" He demanded, using that tone of voice that usually got him answers. The scientist jumped at his tone and turned to face him. There was a lost look on McKay's face that made his stomach suddenly start hurting.

"He didn't leave the city. I checked the stored data. The satellite over the city didn't record anything leaving since our own jumper left."

"Maybe he went through to the Alpha site instead. Maybe something happened there."

"Oh and he wouldn't drop a word about that to us? Just maybe casually mention that he wouldn't be home for supper…for three months or so." There was the snark that Ronon expected.

"Don't borrow trouble McKay. He might not have had time to contact us. If something was happening there he might have had to go through immediately. You said that Atlantis was closing down non-essential things. Maybe that included communications. He might have tried to call and couldn't reach us. He'll show up on the Daedalus when they get here in three days or so." The earth ship was due at the Alpha site in the next day, and the plan was for it to come to Lantea after that. After that the large ship would only make the trip every three weeks with supplies and new personnel. McKay stood up and pushed past Ronon toward the door.

"I don't have to borrow trouble, Conan. Sheppard has a permanent lease on it. Communications were going to be one of the last systems to go. No matter what might have gone on at the Alpha site there is no way that he couldn't take a moment to let us know he wouldn't be coming." The scientist was striding toward the open area where the jumper was sitting. Ronon followed.

"Then where is he?" Ronon was pretty sure that McKay was right. Sheppard would have let them know if the plan had changed. He also knew that only left one place Sheppard could be, but he still wanted to hear it from McKay. The scientist answered in a hollow voice, without stopping his progress.

"He's still there. He's still on Atlantis, and that's where he's going to stay for the next three months. Alone."

Chapter 5

Waking up, for John Sheppard, was not a pleasant process. His head was pounding, his throat hurt, he was cold, and his bed had somehow become like a rock. He tried to move, to find a more comfortable place, and go back into the darkness from which he had come, but it was not to be. Something was nagging at him. After lying there for some time, floating in that place in between waking and sleep, it finally hit him. He was wearing a vest, his boots, and if he wasn't mistaken his holster. There was no reason that he would have gone to sleep wearing all of that. He moved an arm, and he felt it then, pins and needles. His mind suddenly kicked into high gear.

He had been hit with a wraith stunner! He had walked into the lab, expecting to be told about some problem or another, and that bastard had shot him. He was never going to let Rodney live this down. Obviously one of his lab monkeys had cracked under the pressure.

Sheppard pried open one of his eyes, and rolled onto his side on what he now realized was the floor. The movement, accompanied by the pins and needles in his arms and legs, seemed to waken the cough that had been plaguing him all day. He coughed and coughed, his throat feeling like someone had taken a piece of sandpaper to it. He also noticed that now his chest seemed to have gotten involved as what felt like two bands of iron had been clamped around his chest. That was probably not a good sign.

He managed to force himself to his hands and knees and hung there for a moment, waiting to catch his breath. As he did so he realized that he must have been unconscious for quite a bit longer than usual with a stun blast, otherwise the pins and needles would be worse. Compared to the last time he had been hit, he figured it had been at least an hour maybe more like two. Not that he minded missing out. There was something about time however. Oh sh…!

When he had walked into the lab they had been less than 30 minutes from total evacuation, less than an hour from Atlantis returning to her watery bed, for a long nap. If he had been unconscious for two hours…he forced himself up onto his feet, stumbling to the lab table to hold himself up. He noticed that the computer that had been there, along with the scientist, was gone. No, this was not good. It came to his attention that the lighting was at minimum, just above the darkness that had enveloped Atlantis when they had come. It was so different from what he had become used to.

He stumbled toward the door, his hand instinctively dropping to confirm that his pistol was still there. He had left his P90 in the control room, but at least he was armed. He had a feeling it wasn't going to matter though. Atlantis felt…different.

It wasn't like when they had arrived. Then, there had been a surge of something, almost like a low-grade electric buzz in the back of his head, down at the base of his brain. It was a feeling that had stayed there every day since then, except when they were off world. It was a feeling that surged through him anew each time he returned from the mainland or another world. It had grown since the first time, each time he was gone, it seemed to intensify when he returned, as if the city was reaffirming his place there. He wondered sometime if any of the others felt it. He suspected not, as someone surely would have mentioned it.

Now, he could feel only a small portion of what was usually there. It was like a tickle, barely there. That told him that Atlantis had already shut down. The non-essential functions that McKay had spoken off must surely include whatever it was that reached out for the descendents of her lost creators. Maybe an ancient would still have been connected, but he was too far removed in time and genetics.

He managed to stumble his way to the control room, finding that the transporters were off line, and having to take the stairs all the way, almost ten minutes later. As he had gone the lights had followed him. Turning off as he left one section, and turning on as he entered the next. He was starting to feel like he was in some weird sci-fi movie, and something was lurking in the darkness beyond the ring of light that he stood in. Shaking off that thought he continued to the control room and found what he expected to find. A darkened room, that lit slightly as he entered, but otherwise empty.

The stained glass windows that the sun lit so gloriously were dark and the consoles, without the human computers and add-ons, were covered by the same dust cloths that they had removed at their arrival, nice touch that. The big screen behind the main consol was dark, no data or schematics on it now. Everything was dead, and he was entombed with it. The city had sunk, the shield was up, and he was trapped here for the next 90 days, alone.

He sank down onto the stairs, putting his head into his hands. He allowed himself a few minutes to just sit there and let it sink in, to feel sorry for himself, if the truth be told. Intellectually he knew that he could survive 90 days alone. He was not a gregarious person by nature, and he was comfortable with his own company, but still…3 months. He felt as if he had been convicted of a crime and sentenced to solitary confinement. Maybe this was some sort of cosmic karma for all the things he had done in the name of duty and necessity. Of course 90 days was no penance for waking the wraith, or killing his commanding office, so that didn't work.

Why exactly was he here? Obviously the man that he knew as one of McKay's scientists had some reason to do what he had done. He had obviously planned the ambush for when and where it had taken place. He had stunned Sheppard, closed up his computer, and calmly walked through the event horizon to the Alpha site as if nothing was wrong, knowing all the time that Sheppard would not be able to escape the sinking. He had wanted Sheppard to be here. But why, and just how far had he gone to get Sheppard here?

They had been working on the assumption that whatever had triggered the system check had been accidental. But what if it had all been part of the plan? What if the system check had been started to do just what it had done, evacuated everyone. Had whoever caused this wanted him specifically, or did they just want someone, or just a gene carrier, or just a member of the military? What was behind it all? There were all kinds of possibilities, but he was damned if he could think of one that made sense.

It wasn't as if anyone could take over the place while it was locked down under the shields. So, no coups planned ala Kolya. No one could use the star gate to dial in as the systems were shut down. No incoming wormholes permitted. Rodney had said that it was a type of failsafe to keep too much power from being diverted from the process. An incoming wormhole at the wrong time could reset the whole process and it would have to start again, like using your computer while you were defragging it.

Of course someone could be standing by to try to seize the city when it rose again, counting on that lag time between the rising and when the Lanteans could return, but it seemed a long time to wait, and the Daedalus would be dropping by intermittently, a fact known to all, so it seemed an unlikely plan. And it still didn't explain why HE was here. Obviously the man, whomever he worked for, had wanted him to be here, or at least wanted a body here, what possible tactical explanation could there be for that?

He shook off the thoughts of what might be behind all of this, and pushed himself back to his feet. He was going to have a lot of time to consider that, but if he was going to be here for the next 90 days, he needed to figure out how he was going to survive. It was already growing colder in the control room, the large room cooling quickly. It might be on the edge of summer above, but the waters around the city were cold, and they would leach what heat there was quickly. Sheppard could see the formulas for the exchange of heat in his mind, and knew he had been hanging around McKay too much.

First order of business was to find a place to live. His own quarters were on an outside balcony and would not work, too exposed. The control room would have been nice, but it was just too big and cold. He would prefer a more comfy room. He looked thoughtfully at Elizabeth's office, but discarded the thought. She would not appreciate what he was going to have to do to the room. Better to try somewhere else. He did want to be near the stargate, so his options were limited. His eye fell on the small conference room. Perfect.

A little over two hours later he stood in the doorway to the small room looking over his handy work. It wasn't pretty, but it was utilitarian, and it would keep him somewhat comfortable. He had broken up the modular table and moved most of the pieces out, retaining three. Those he had used to form a small enclosed space against an inside wall, having two sides and a top. It resembled nothing so much as a 'fort' he had built out of sofa cushions as a child. Into his fort he had placed a mattress, humped up from the nearest quarters, and after a raid into five different rooms a nest of blankets and pillows. He had been gratified to see that Teyla, wise in the ways of traveling light had left several of her heavy wool blankets behind, and he had grabbed them along with some of the thin military issue that people had decided to leave behind. Even if the temperature dropped into the freezing zone, which seemed likely, he should be good. The tables would help to hold in his body heat, as would the blankets. From his own quarters he brought clothes and toiletries. He was happy to see that the toilets still worked, at least for now. That could have gotten ugly. There was no running water however, and his next concern was going to be food and drinking water.

He had to sit down for a moment in one of the chairs that he had left in the room. His chest had been feeling tighter and tighter, making it hard to breathe, and his cough was starting to move from that dry hack to a croup with more wetness to it, something he was not happy about. It looked like that flu was settling into his chest. The muscle aches had not improved either. The cold was not going to help that. He needed to get some warmer clothes on before he went looking for food and water. He could not afford to get sicker than he already was. Beckett was not going to pop up and give him a shot of antibiotics or a couple of vitamin C, or make him stay in bed and drink not-so-chicken soup.

He had packed only a portion of his clothes for the trip to the mainland. He had figured that they could do laundry regularly, and hadn't figured on needing a large wardrobe. Most of what he had taken had been clothes for a warmer climate anyway, so he had plenty of stuff to put on. Of course laundry was not going to easy here, unless he could find a fresh water source. He had an idea about that, but he would have to look into it after he dressed. He rummaged through his clothes and found the military issue long underwear that he had used in Antarctica. He had known that would come in handy again.

After dressing in several layers, during which he discovered that he was having some definite temperature control issues, he left his room in search of fresh water. He knew there was plenty of seawater, most of it relatively clean, in some of the lower sections. He could, if worse came to worse, distill it to get fresh water. He had taken all the survival courses, and knew the drill. However without a power source that meant he would have to build a fire of some sort, and he wasn't sure what he had to burn. But that was a problem he hoped not to deal with. For now he made his way down to the desalinization tanks where the seawater had been being turned to fresh in a more efficient way. They were not functioning now of course, but it he was lucky, the fresh water tanks would have something in them.

He reached the tanks, and pulled the inspection port on the first one. Shining his flashlight down inside he could see that there was about half a tank. That was both good and bad. He had some water, but this was the last tank. The others two were the primary storage. If this tank was half empty, there was a good possibility that the others were completely empty. He moved to the next, and then next, confirming his fear. Okay, so he had half a tank. He eyed the tank, mentally measuring the circumference and estimating the height of the water. Quick mental calculation gave him the volume of the column and another the possible amount of gallons enclosed in that space. Not great, but then he wasn't planning on filling a swimming pool or anything like that. He had found some clean food grade plastic bottles in the kitchens, three gallons each, and he quickly rigged a way to lower the bottles into the tank, filling them. That should be enough for now he figured, mentally subtracting the amount from his total. It looked like any bathing he did was going to be in seawater. He had a feeling that he was going to be ever so slightly offensive by the end of ninety days. Maybe he would be able to squeeze in a shower before everyone showed up. In fact, he was feeling more than a little sweaty right now. He had been cold before, the layers of clothing feeling good, but now he was sweltering. The slight activity of filling the jugs should not have caused this.

He was going to have to face it he was not getting any better. He needed to find what food he could, and maybe see if there was some form of light that he could set up independent of Atlantis. If any more systems went down, he didn't want to be literally in the dark. Then, he was going to crawl into his nest and sleep. All he needed was a good rest, and he would be feeling better.

Food proved to be somewhat more elusive than the water. The kitchen was cleaned out down to the last crumb. He felt like a poor church mouse, hunting hungrily through the empty cabinets. Once he had verified that the cooks had been very thorough in cleaning out their domain he moved down to the storage rooms. They hadn't been able to take everything with them to the Alpha site, and he found what he was looking for there, though he wasn't overly enthused. He the MRE packets from the Jumper, enough for a month, five cases of twenty emergency ration bars, and wonder of wonder, a handful of chocolate chip power bars. How had Rodney missed those?

The ration bars' claim to fame was that they supposedly packed a days worth of calories in one small shortbread like bar. Easy to store, long shelf life, practically indestructible packaging, and to Sheppard almost completely inedible. They were too sweet, too dense, and just on the edge of nauseating. However, since he had only a month's MREs he was going to have to make do. The power bars could be a weekly treat, at least for a while. He was also going to have to check the living quarters. He didn't want to invade anyone's privacy, but he was sure that there was a good amount of food still stashed in rooms throughout the base. Hell, McKay's room might feed him for a month depending on if the scientist had had time to pack or not. Cheered by the thought of illicit chocolate and who knew what else from his friend's hoard, he picked up the cases of MRE and one of the ration bars, and with the power bars balanced on top, headed back to his new digs.

He stacked the boxes of food next to his water supply, and sat down for a moment to regain his breath. It was with some trepidation that he realized he could now see his breath in the cooling air. The temperature had dropped radically. He vaguely remembered one of the oceanographers explaining about he deep cold current that flowed under and around, and now over, Atlantis, about how it came directly from the poles, heading toward the equator where it would be warmed. Obviously with the power shut down the heat was leaching very quickly. He had not realized how much energy the city must have had to expend in those ten thousand years of waiting just to keep the place livable for people who would never return. At least they had benefited from it when they had first come.

He had just a few more things he wanted to do before he took to his bed. First he wanted some Tylenol or at least something to take the edge off the muscle aches and maybe help with the fever that he suspected was causing his temperature issues. He figured the jumper first aid kit would help him there. He needed to go there anyway for the lantern he wanted. It ran on both batteries and on a hand crank, so he should be good to go. There was also a small stove and some cooking gear in the jumper too. He would need those eventually too, though right now he was not hungry.

He glanced at his watch. It had been barely four hours ago he had woken to find himself trapped here. He wondered what his team was doing now? He knew that as far as Teyla, Rodney, and Elizabeth were concerned he was on the mainland with the others, preparing to take it easy for three months. Ronon and the others must be pretty upset though. They would not know what had happened to him. Would they think he had gone to the Alpha site? Had crashed into the sea? Gotten trapped on Atlantis? Well, the last was right, but he bet they wouldn't guess why.

They had a jumper and a pilot, so he figured they would come looking, sooner probably rather than later, but the question was what could he do to show them that he was here? And, how would he know when they were there, if they hadn't already come and gone. It wasn't like he could blink the porch light. Looking up a the dim light that Atlantis was providing him, he doubted that anyone would spot it even if he were in one of the windowed rooms near a balcony. He was going to have to find a place close to the edge of the shield, and find way to leave a message. But he could not do it now. He just didn't have the strength even though it irked him to admit it.

He dragged himself out of the chair and went toward the hanger. The lights barely came up enough to let him see the jumper, but the flying machine itself lit up like a Christmas tree when he stepped inside. It seemed to be showing off almost, making him smile. He quickly scrounged some pills, swallowing them with some of the bottled water in the supplies, and then turned to gathering what he wanted to take. He made up what should have been an easy to carry bundle, and found out that it wasn't anywhere near easy. His back felt like it was breaking and he had to stop and catch his breath twice on the trip back. He just dropped the whole thing near his food and stumbled to his improvised bed. He fell into it, and managed to take off his boots and climb under the pile of blankets before he succumbed to the utter exhaustion that seemed to wash over him like a wave. He didn't notice when Atlantis turned out the lights.

Chapter 6-

Okay, this was getting tedious. McKay brought the jumper around for another pass under the city. Still no openings or weakness he could exploit. He knew that since the jumpers were meant to be used both above and below water there had to be some kind of shield that was used that would allow the jumpers to exit and enter even when the city was underwater, sort of like what they showed on space shows when they launched shuttles. Vacuum and water were not that different, and he was sure that the ancients had worked out the process. He just wished they had left a little something about it in one of the databases that were in the jumper. This was the forth or fifth pass they had made around the city, and so far they had found nothing, not even an indication that the city had any power or activity at any level. Three hours and nothing!

He didn't want to consider what it might be like in there for Sheppard. If there was no power at all it would be dark and it would be cold, and there would be little the colonel could do to change that. There should be some water in the desalinization tanks, but he wasn't sure how much. He had seen that they had purged most of the water early in the process, though there had been some. Neither he nor Zalenka had been able to find out just how far down the systems were going to go. There might be some lights but certainly no heat. He brought up a HUD, with the temperature of the surrounding water. Just above freezing, crap. That meant the city was going to loose heat quickly. It was never really warm there. The ancients had obviously preferred a slightly cooler climate and temperature than modern humans.

And what about food? With his allergies and hypoglycemia McKay was more sensitive than others about food. He tended to worry when his next meal was not planned out and readily available. What did Sheppard have in there? He knew there was some in the jumper, but not 90 days worth. Was there anything left in the stores? It wasn't like Sheppard could hunt or even fish, though there might be something swimming around down in the flooded sections. The biologists had babbled something about a natural reef and new habitat, but McKay hadn't paid a lot of attention except to make a mental note not to go in the water when exploring the lower reaches. Would Sheppard think of that? Of course he would. The man was trained to survive, though McKay was sure that being stuck inside what amounted to a ship in a bottle was not covered in whatever survival course the Air Force might have.

In the copilot's seat Ronon was watching the city go by, looking for any lights that might indicate Sheppard's presence. So far the big man had been pretty stoic about the whole thing, but McKay could sense the impatience building under the quiet exterior. He wished, for the umpteenth time, that Teyla were here with them. She would have been a calming factor that was sorely needed, and not just by the Satedan. McKay could feel the mild panic building inside himself. His friend was trapped in a millennia old computer that was resetting itself, and would be there for the next 89 days. Why shouldn't he panic a little?

He brought the jumper around and angled up toward the surface. There was nothing more to do here. He needed to go back and look at the specs he had on his laptop. There had to be somewhere on the city that the shield came close to the city itself. Sheppard would know that they would be worrying, and would try to leave some kind of message, or make an appearance. He would be looking for such a place, and Rodney intended to be there when he found it. They broke the surface and flashed into the sky, heading toward the mainland. Ronon looked around at him.

"What now?" He asked. McKay took a moment to be slightly offended that once again he was expected to solve all the problems, but then accepted it as his lot in life.

"I need to look at the schematics. There has to be somewhere that the shield comes close to somewhere that Sheppard can get to. He might be able to leave a message or something."

"How do we get him out?" Oh well, there was the question he had been waiting for.

"We don't. At least not anytime soon." He could see the angry look on Ronon's face even as he concentrated on keeping the jumper on a straight course. "Look, the shield was made to hold back an ocean. It isn't as if we can just blow a hole in it with a drone and pop in and get Sheppard. If we breach the shield we literally sink the city. Somehow I don't think even Sheppard would expect that. No, at this point the best we can hope for is to make sure that the man is still alive in there."

"Why wouldn't he be?"

"Why would he be stuck in there in the first place? The man may have no sense of direction, but he can certainly tell time. There is no reason that he should have been there when the city sank. As soon as the last person went through the gate he was supposed to take off, and even then he should have had almost half an hour to do it. If he was stuck there then something went wrong, and with Sheppard it always pays to suspect the worst."

"Some kind of invasion?"

"Not that worst, Conan. I'm talking falling down a flight of stairs, or tripping over his own feet and spraining an ankle, or bumping into an ascended princess and stopping to make time. You know, the regular things."

"What if the jumper broke down?"

"There was nothing wrong with the jumper!" That was just impertinent. McKay and Zalenka had gone over them not a week ago. All of them were in top condition. He saw the small smile on Ronon's face and knew that Satedan had been trying to get a rise out of him. "Oh very funny. Are you taking over Sheppard's oh so very amusing 'blame the scientist' game? Why couldn't you learn something useful from the man like…well there must be something good that you could have picked up." The two shared a small smile. Then the situation reasserted itself into McKay's mind and the smile faded. He focused forward again bringing the ship back on course since it had wondered…just a little.

"He'll be okay. There's water, and there has to be some food there somewhere, if nothing else he can raid Elizabeth's stash of dark chocolate that she had in her office. Though I think she changed her hiding place after we found that last stash."

"Nope, I found it last week."

"And you didn't share? I call that team spirit."

"Shared with Teyla."

"And is she your only teammate?"

"She was the only one that was harder to spar with than usual last week. Sides, chocolate won't make you any better." It took a moment for McKay to figure that out, and then he shook his head and waved a hand.

"Too much information! There are things about the three of you that I do not want to know, and that is one of them." They were over the camp now, and he brought the jumper in for a landing. If it was a bit harder than Sheppard's who was going to tell him? He bailed out as soon as the ramp was down, waving off the inquiring marines and doctor and heading for his hut. Let Ronon fill them in. He stumbled to a stop as his eyes fell on the bunk and duffle that still sat to one side, but then he shook his head and went to his laptop.

He was already going through the schematics when Ronon came in several minutes later. He scanned each one then discarded it when he didn't find what he was looking for and moving to the next. There was a very large amount of them, and it had to be the right place. Somewhere Sheppard could access, somewhere there was some way of leaving a message, somewhere they could just see him, make sure he was okay, that he hadn't broken his fool neck or something…He stopped scanning and bowed his head. Ronon put a heavy hand on his shoulder. The Satedan didn't say anything, but McKay nodded in gratitude and went back to work.

Chapter 7-

He didn't know how long he had been asleep, but things had not improved with him since then. He was hot, and cold, and…just not right. His chest was tight, and as he woke, he had to curl up on his side and ride out a series of wet coughs that had him spitting a nasty wad of mucus into a piece of paper his scrabbling hand found on the floor. He hoped that hadn't been anything important. He was barely aware that as he coughed the lights came up slowly to a level that seemed just slightly less than before, or maybe he was just that much more bleary-eyed. Once the coughing spasm passed he just lay there, curled on his side and tried to get up enough energy to sit. That didn't seem to be working out well for him. This flu was really kicking his butt.

He knew he needed to get up, get some water and food, and probably see if there was anything left in the infirmary that could help. Maybe some kind of cough syrup or something to help clean the stuff out of his chest. He suspected he was in for a few very uncomfortable days. He sat up, legs splayed out over the floor, and shivered as he moved out from under the blankets, definitely colder now.

He looked at his watch his mind only partially noting the time then did a double take that would have been comic in any other situation. According to the calendar it was a day later than when he had gone to sleep, and almost the same hour. He had slept almost 24 hours. He needed to get moving. The others on the mainland would have come and gone already, and he had just been lying around. They would be worried. He was glad only Ronon was there from his team, the Satedan would be calmer than McKay would have been. Of course Teyla would have been calm, but probably anxious. At least they were being spared that.

He stumbled to his feet, swaying slightly as the head rush threatened to put him back down. He leaned a hand onto the wall, and almost fell over when what felt like an electric spark shot up his arm. What the hell? He tentatively reached out again, pulling his hand back twice before he actually made contact. When he did finally do it, there was no sensation at all, not even the warmth that he usually felt. Very strange.

After getting a drink of water and ignoring the food stacked beside it, he headed toward the infirmary again. He didn't usually mind the walks between different parts of the city, but now, he really wished for the transporters. He arrived winded, stumbling, and weak. He had to make use of a handy bed for a few minutes to catch his breath and recover from the walk. When he went to get up, another coughing jag hit him, and once again he brought up some mucous. At least here he had some Kleenex. He was getting ready to toss the mess in the nearest trash when he noticed the color of the tissues. They were red. He peeled them open to look at the slimy mess, an action that made his already puny stomach all the worse. The mucous was greenish with blobs of red. Damn. He had pneumonia. He had seen this before, and he had heard Beckett mentioning bloody mucous from the few people who had developed it from the flu. He threw out the tissues and headed toward his goal, a bookcase lining one wall of Beckett's office. The man had obviously not taken hardly any of the volumes he regularly kept, if any. Sheppard skimmed through, looking for the one he knew was there, finally spotting it near the bottom next to a series of books on something he could not even begin to pronounce. He reached for it and took it out, sinking into Beckett's chair gratefully. He peered at the book in the dim light.

The Witchdoctor's Guide to Everyday Medicine had been presented to Beckett as a gag gift at the last Christmas exchange. It didn't take a genius to guess which genius had gotten it for him. The giftgiver had expected outraged huffiness, but had been sadly disappointed when the gift receiver had looked through the book, and declared it a good layman's guide to minor medical issues. Beckett had gone on to say that the book had practical, easy to understand listing of symptoms and treatments, and instructed the reader when an actual doctor should be consulted, despite the title. Sheppard was hoping that it could help him now. Knowing that he had pneumonia was one thing, knowing what to do about it was another.

It didn't take him long to find the chapter on lung issues and soon he was reading through a list of symptoms. He was glad to find that it appeared he had the viral type of pneumonia, not the bacterial which was much more serious. However, there was no real treatment besides taking something for the fever and muscle aches and getting a lot of rest. Seeing as how just sitting here was making him tired, he didn't figure the rest thing was going to be a hardship. He was going to have to force himself to eat however, and find some more Tylenol.

A quick check of the storage showed that the pharmaceutical locker was empty. No surprise there. He had about three more doses in the first aid kit from the jumper, and maybe the same in his quarters, but that was it. The book said that this could last up to a week, and he needed the pills. It was time to go a-roving through the quarters. He needed to check for food anyway, so he guessed he could check for pills at the same time. He just wished he didn't feel so bad.

He knew he needed to see about getting a message out, but the very thought of walking almost anywhere but back to his bed was tiring. They would have to wait. He decided to get the things out of his own quarters first and then tried McKay's. He hit the jackpot for food: five more power bars, the peanut butter kind; two MREs; three packets of cream of chicken soup; some saltines; and what appeared to be an unopened box of Malomars made up his bounty. Oh he was so going to have to mention this to McKay. The man was amazing. He stuffed it all into a duffle he had grabbed in his room.

He then moved on to Teyla's and then Elizabeth's quarters. He felt somewhat better about violating their privacy rather than someone else's. He didn't think anyone would begrudge him the stuff, but he was uncomfortable in any event. He found a bottle of what appeared to be a pain killer in Elizabeth's medicine cabinet, though it seemed to be 'made for a woman'. He figured that the painkiller wouldn't know he didn't have ovaries, and dumped it in his bag of booty. In Teyla's room there were not any painkillers, but he did find a stash of chocolate and some of the stout tea that the Athosian drank in the morning. That stuff would burn the pneumonia out of him. He hit Beckett's room next, finding a bottle of Tylenol and some aspirin as well. That might be best for the fever. He ignored Ronon's room, knowing that the big guy traveled light, and had probably packed everything anyway. Having ravaged the quarters of his friends, and feeling about ten times worse than when he started he decided to call it a day, even though he had been up for only a little over two hours.

He returned to his nest, and reluctantly put a small pot of water on to boil. Once it had done so he dumped in one of the soup packets from McKay's room and stirred it up. It was not appealing looking, and it probably would have tasted better if made with milk instead of water, but it was hot and it soothed his throat on the way down. His stomach wasn't all that enthused about it, but it stayed down, and he took a couple of aspirin with it, figuring the food would buffer the acid, and carry it into his system quicker. That done, he curled up on his side and just lay there for several minutes, eyes open, but not really seeing anything. In that floating, half-conscious mode he suddenly felt something tingling along his nerve endings. It was a…thrumming, coming in waves of sensation that seemed to hit him like water surging against a beach. It wasn't unpleasant; in fact it seemed to be easing his muscles, not unlike a massage. He managed to pull his boots off, and unconsciously rocking to the beat of the strange waves, he buried himself back under his blankets and let himself drift on the surge and fall.

He knew he was dreaming almost immediately. First off, the gate room was filled with light, shining gloriously down through the stained glass. Secondly the room was filled with people he had never seen before, dressed in a manner that he recognized from the few descriptions he had read as that of the Ancients. The people were moving to and fro, ignoring him standing in the middle of it all, dressed in his usual black on black, and standing out like a sore thumb in the pastel colors of the others. He was standing in front of the stargate, which was engaged, and he watched as wave after wave of people passed through the gate, all outgoing.

It struck him as they did so that he was watching the first evacuation of Atlantis, ten thousand years before. This was it, the final solution for the Ancients in their fight against the wraith. Run and don't look back, don't be concerned about all those who you left behind to face the wrath of the predators. Or this was at least a representation of that, how his mind envisioned it from the stories that the other Elizabeth had told, and what they knew to be true. But why was he here, and if he was having fever dreams, why was he lucid enough to recognize the fact?

"Because we wanted you to see." Came a voice from everywhere and nowhere. None of those around him seemed to hear it, or they were giving a good impression of ignoring it.

"See what?" He wasn't sure who he was asking, though the voice sounded familiar, almost hauntingly so. A memory deep within him stirred

"Your beginning…and our end, or what we perceived to be our end until you came." Okaaay, that was suitably vague. He looked around, but no one seemed to be paying him any attention. Certainly there was no one speaking to him. He wondered toward the control consoles where he noted there seemed to be a conference in progress. One man in particular took his attention. He was dressed differently than the others, in dark brown, and in a more austere and practical fashion than the sweeping robes of the others.

"Yes, you would be drawn to him. Everyone was. Evidently that too was genetic and has passed down in the blood." Oh good, that cleared up everything.

"Well I wouldn't say it was love at first sight or anything. He just seems…familiar." It was true. Just as the mysterious voice was familiar, the man standing with folded arms listening as a tall robed woman spoke, was as well.

"Indeed. Blood calls to blood, even across the eons." Blood? Okay that was enough of the vague stuff. He was tired of it already.

"All right, now that one I gotta call you on. What the hell are you talking about, and where the hell are you?" He had read somewhere that in lucid dreaming you were supposed to ask questions to get the most out of the experience, since your dreams were supposed to be trying to tell you something.

"We are here, John." Came the voice from behind him, and he spun, and almost fell over as he saw her standing there. As it was he staggered back and into one of the clear, bubbling columns. He could feel his face going pale. He stumbled away from her, and without any thought turned and ran.

Almost ten minutes, or whatever the dream equivalent was, and two transporter trips later he pulled up on the farthest point he could reach and still be on Atlantis. He was breathing hard and sweat dripped into his eyes. He had never run so hard or so fast, not even in Afghanistan, never except for one other time in his life. A time he had tried to put out of his mind.

He stood on the end of the east pier, looking over the water, and trying to calm his breathing. He dragged an arm across his forehead. The wind battered at him, almost tearing the soft jacket off his shoulders. He pulled it back on, and stopped. He hadn't been wearing a soft jacket…He looked down at himself. He was wearing almost exactly what the man in the gate room had been wearing, except his outfit was black. How the hell…Oh right, dreaming.

"You cannot run here, John. There is nowhere that you can go that we cannot be. In a way there never has been. Face us." For a moment he contemplated jumping into the water and doing his best to swim to the mainland. It was only a couple hundred miles. He could make it. But even in his dream he could not be that much of a coward. He straightened up, took a deep breath, and turned.

She stood about ten feet away from him, dressed in the white robes that the rest of the people he had seen had been wearing, her short dark brown hair blowing in the wind. The wind that suddenly felt incredibly cold against his back. Great, even in his dream he was having temperature issues. Her hazel eyes were locked on his, and a gentle smile curved her lips.

"Always our brave boy." She murmured. He slashed a hand through the air, anger replacing the...whatever it had been that had sent him running.

"You are not her," he growled, his teeth clenched. He had to hold tight to his anger, or he would be overwhelmed. "You are a construct of my mind, my feverish mind I might add. Delusional here."

"Not so much as you might think, John. Though you are ill, we are most concerned about that. Your healer is not present and cannot aid you. His medicine is primitive, but effective for the most part. Our own systems will not reinitialize for another two of your months, so we cannot aid you ourselves." It was the precise way she spoke perhaps more than the repeated use of 'our' and 'we' that clued him in, though he already knew she wasn't who she looked like.

"We?" He asked, edging to the side, toward the doors. Though where he was going to go he didn't have an idea. He was in a dream, and like 'she' said, she could go anywhere he did here.

"Please do not run, John. It is not restful for you. Your body needs what rest it can get to fight the illness. If your mind is unsettled, you will not get any quality rest."

"Thanks for your concern. Now, who are you?" The smile came again, and a chill that had nothing to do with the wind chased up his spine.

"We are who we appear to be."

"No. No you're not." He wasn't buying whatever 'it' was selling.

"As we were to those who you saw here, so are we to you." Okay, that took some thinking. But still…

"Look, I don't know what this is about, but I'm dreaming right now and if I'm supposed to be learning something here, I'm missing the point. Can we get to it without all the…" he waved at her, conscious of the fact that the was sounding ever so slightly like Rodney McKay.

"Actually you are not dreaming in the sense that you intend its meaning." That stopped John's slow progression toward the door. He looked at her with suspicion.

"Exactly what would I be doing then?"

"You are joining; as it was meant to be. You were not present at your birth therefore you did not join properly. When the system reset occurred, and you were present, it allowed an opportunity. We could not ignore it." Now he reversed course and strode toward her.

"Joining what?" He demanded. If this was some kind of mental attack, some new weapon used by one of their enemies…He loomed over her, but she was not cowed.

"Be calm, John. No harm will come to you from us. We are here to nurture you, as it should have been from the beginning. We could no more harm you than ourself. It would be against everything we were created for. Had you been joined from birth, you would not have ever known the loneliness we see within you. You will not know it again." She reached out and laid a hand on his cheek before he could back away. There was a spark of something like electricity that crackled through his body, making his head spin and felling him to his knees. Without removing her hand she knelt in front of him, her hazel eyes, mirror images of his own, were locked on his. Darkness seemed to be closing in on him from every direction, leaving only those eyes, burning into his soul. He struggled, but he could not push it back. He felt a hand in his hair, and it felt so good, so familiar, he could not stop from leaning into it. It had been so very long.

"Rest, John. There is nothing to fear, our precious one." A voice said from all around him, a voice he had never thought to hear again. He stopped struggling and fell into his mother's arms.

Chapter 8-

It had been three days since Atlantis had sank back under the waters, and Rodney McKay had slept about six hours in that time. He was hunched over his laptop, where he had been almost constantly since he had begun searching. The only time he was away, except for calls of nature and the occasional face plant into his mattress, was when he piloted the jumper to the city to hover outside one place or another, checking for any sign that John Sheppard was alive. So far there was nothing.

Food and coffee had miraculously appeared at his side, and he wondered how he could get that to happen when they went back to Atlantis. He had also acquired a shadow in the form of one tall Satedan who sat quietly in the corner of the hut, honing one knife or the other, or sat in the co-pilot's seat, staring at the city as if he could see through the walls to the man they sought. He had found three points on the city so far that were promising, but when they had gone to see there had been nothing, no Sheppard, no message, just…nothing. He was scrolling through the next set of diagrams when a sound from the communications array almost made him jump out of his skin.

"Atlantis mainland this is the Daedalus, do you read?" the voice boomed out. McKay hastily reached out and lowered the volume on the speaker. He flicked the switch to send.

"Daedalus, this is Atlantis mainland. We read you. Is Colonel Sheppard aboard?" It was a long shot, but there was the barest possibility that he could have been wrong about Sheppard calling first before he had a change of plans. Of course if that were the case he would have to kill him, but at least this hell would end. There was a long pause from the other end and then Caldwell's voice came from the speaker.

"Atlantis mainland, this is Caldwell. It was our understanding that Colonel Sheppard was there. Should we take your question to indicate that this is not the case?" McKay rolled his eyes.

"No, I just thought I would ask. I haven't seen him for a while, and I thought maybe he dropped by to chat and have a cup of coffee. I just wanted him to stop and get a loaf of bread on his way home." He snarked. He could almost see Caldwell's face screwing up in that scowl he seemed to get as soon as he set foot on Atlantis. What was that about anyway? "No, he is not here. There was the outside possibility that he might have gone through the gate to the Alpha site instead. I'll infer from your response that he did not do so." So much for that faint hope.

"No. As far as the Alpha site is concerned, at least when we left, Colonel Sheppard was here. Could he still be on Atlantis?" McKay had to bite his tongue not to reply snarkily to the question. Pissing off Caldwell, while worthwhile on principal, would not help the situation. This was how low he had been brought. Sheppard owed him big time.

"That is the hypothesis upon which we are working, yes. However since we cannot access the city via communications or computer and there has been no visual confirmation it is just a hypothesis." He went over his efforts so far, and the results of his playback of the satellite information.

"And there is no way for him to get out of there? He's just stuck there for the whole ninety days?" Caldwell concluded when McKay was finished.

"Unless Hermiod has made some startling discovery enabling the Asgard beaming technology to penetrate the ancient shields, yes he is stuck there."

"Does he have food and water?"

"Water is a very good possibility. There should have been some in the desalinization tanks, even after the process shut down. He'll know to look there. Food is more problematic. There has to be stuff in people's quarters, but I don't know about storage, or how much. Lorne had lists of everything, the manifests; he should be able to tell us if there was anything. Can you boost our signal back to the Alpha site?" Caldwell must have conferred with his comm. tech as there was another delay then…

"Atlantis Mainland, this is the Alpha site. How do you like your camping vacation, Rodney? " It was Elizabeth's voice, and McKay was almost reluctant to reply as Caldwell had obviously not filled her in on what had happened, or what they thought had happened. This lack of empirical data was frustrating as hell. "Rodney, are you there?"

"Yes, Elizabeth, I'm here. Camping is just peachy. It's everything I knew it would be, bugs, sunshine, cold nights, a missing Colonel, bad food, and smelly companions." He was pretty happy with how he had just slipped that in there. There was another delay. He had to contain the desire to tap the microphone.

"What do you mean a missing colonel?" Even over the distance Elizabeth's voice took on that rather strident tone that she tended to get with the SGA-1 team on a regular basis. He hadn't noticed before just how harried that tone was.

"Sheppard didn't make it here after the city sank and since Caldwell says he isn't there, we can only assume that Calamity John has struck once again and that he is on Atlantis."

"But you said everything was shut down for 90 days. How will he survive?"

"That's the question isn't it, along with why the hell didn't he leave when he was supposed to? We need to talk to Lorne who had the manifests and see if there is any food there, beyond what might be in the personal quarters. He should have water, and he can bundle up against the cold. It's probably going to be dark, but there are lanterns on the jumper, and flashlights. Sheppard's had survival training he's probably all set up with a complete camp by now and is sitting there reading War and Peace by lamplight while we worry about him… " He stopped talking as he realized he was just babbling now, trying to make himself feel better

"But why would he stay there? The last of the marines through the gate didn't report any problems, and he should have had plenty of time to leave. Could something have happened to the jumper?" McKay couldn't even scrape up enough energy to get upset at the suggestion that the jumper was at fault.

"Zalenka and I did maintenance on all the jumpers last week. Everything was working fine. There're only two reasons he would have stayed. Either he didn't want to leave or he couldn't leave."

"Could he have gone somewhere else? Dialed somewhere else? Could something have changed in the shut down process that required him to stay behind?" Elizabeth was obviously working in that denial zone as well.

"He could have dialed Earth and decided to go and spend the next 90 days in Hawaii, but why would he? Well other than the bikinis, and the food, and the surfing, and well he wouldn't have done that anyway. As to any other planet, why would he bother? The gate was open to the Alpha site if he couldn't get out of the hanger for some reason he could have just gone through to you. As to the shut down process changing, no. The ancients were rather anal about their computer procedures. Things proceed on a set criteria, and they are not going to vary."

"Something happened to him then. He was sick. Could he have passed out or something?"

"You'll have to ask Carson that one. He was the one reading the chicken entrails and casting runes at him earlier in the day. Surely he wouldn't have let him loose if he were going to keel over the first second that he was out of everyone's sight. You also need to talk to the marines that were left, see what they remember. Where he went, what he said."

"I've got Teyla getting Lorne and the marines now. We should have some answers in a minute. How are the rest of you?"

"Other than wondering if all the effort in turning Sheppard into a reasonably useful person has gone to a complete waste, things have been stunningly entertaining here. The local mosquitoes seem to have a marked preference for our insect repellant and I'm pretty sure that I heard one of the marines squealing like a little girl when he spotted a lizard on the side of the outhouse, a structure that I hope never to have to visit again after this little sojourn. If I ever find out who the hell set this thing off I will personally ship them back to Earth in a packing crate. Other than that, we're having a wonderful time. How is the Alpha site, I hope it's not too much of a hardship for you all having to share a space the size of what, the pentagon?"

"Point made Rodney, however I would like to remind you that you asked to be allowed to stay on Lantea, you were not ordered to do so."

"Yes, well put it down to temporary insanity. If I try to do something like this again lock me up in a nicely furnished room with catered food and water on tap. And that's another thing…" He ranted on about the lack of running water and did a second run on the sanitation issue, knowing that she was simply indulging him by letting him let off steam. When he ran down she spoke.

"Lorne and the marines are here Rodney. Teyla has told them what has happened. Lt Minter, you and your men were the last ones off Atlantis were you not? When did you last see the Colonel?

"I, personally, was the last one through ma'am, and the colonel was no where in sight. I last saw him about…fifteen minutes before that. He was in the gate room double-checking our personnel lists. He said something about needing to go get something from his quarters, and he started out of the gate room. I was called away to help with something from medical at that point and that was the last I saw him."

"He got a call, on his radio L.T." Came another voice that McKay figured must be one of the marines. "I was on the door and I saw him take it. He told whoever it was he'd be right there, and ran out. He was frownin' and goin' somewhere fast. You know that kinda intense look he gets."

"Well that's helpful. The man in charge of moving everyone off the city got a call that seemed urgent and left quickly. Maybe, and this is just a stretch, something went wrong somewhere?" McKay suggested.

"I would have heard about it, if it was an emergency, sir." Minter broke in again. "The colonel was on and off the city, and everyone knew to call me with anything important."

"Then whoever it was wanted him in particular." That was Lorne. "Maybe we need to be asking the scientists that were there at that time. Lt. Who was still there?"

"We had about five people from medical, but they were all in the gate room right after the colonel left. He had called down and told them to get a move on, and they had done it. I helped them get the last of their stuff through and checked them off not long after that. At that point it was just my boys and the scientists watching the computers."

"This is Caldwell." The Colonel broke into the conversation. "How many of your men were there, and how many scientists and where were they at that time?"

"I had twelve men, sir." Minter reported. "It was me and two men in the gate room and the rest were doing the last sweep, per the colonel's orders. They were in pairs, sir. The scientists were in several different labs. There were seven of them. They left just before we did. None of my men would have called the colonel sir, not without going through me first. I can tell you that for sure."

"Then it seems we need to talk to the scientists. Major Lorne, you take care of that, immediately." Caldwell ordered.

"Just a minute, Colonel. Not that I don't want the Major to make inquiries, but this is my second-in-command we are talking about, and we will handle the investigation."

"On the contrary, Dr Weir. The military commander of a very important base has been at the least, compromised, and at the worst, killed. That is very definitely a military matter. This could be the first step in a planned takeover or could be a strike against the colonel personally. He does have enemies here in the Pegasus Galaxy."

"I don't mean to interrupt your power struggle here, " Rodney broke in, sarcastically "But we need a little bit more information before we kill Sheppard off or have a battalion of Genii hiding in a boat ready to take over the city when it rises again. Right now we need to focus on getting a message inside, or being able to scan inside the shields to determine if…to make sure that he is still alive. On that note, before we started on the conspiracy theories, did anyone bother to ask Lorne if there is any food there for Sheppard to live on?" There was a short delay during which McKay had to get up and pace.

"We took most of the food. There's probably case or two of MRE scattered around the quarters and at least a few cases of emergency bars. It won't be much, but the colonel will have something."

"Yes, he can starve to death slowly instead of all at once." McKay sneered at the false cheer, not bothering to broadcast it, he saw Ronon look at him, and shrugged. Even he did not like the compact survival bars, even if they were supposed to give you enough calories for a day. He picked up the microphone.

"Okay. So he has food…of a sort. Now we have to get to the rest. It's been three days. By now he should have been making some kind of attempt to make contact with us. He knows Atlantis better than any of us, he should have been in at least one of the places I've tried and left some kind of message. He has resources. He should have tried something by now, even if it was tying a sheet to the railing on a balcony. I don't know about you people but I find that worrying."

"So what do we do? As you pointed out we can't use the beaming technology and the scanners won't penetrate the shields. This isn't a new problem doctor. The scientists at the SGC have been working on breaking through ancient technology for years. It's unlikely that you are going to suddenly have a solution in the next few days, or even the next few months." Caldwell said.

"Perhaps that's because I've been concentrating on, I don't know…keeping us alive for the last three years, and haven't had time to concentrate on shield technology per se. My schedule seems to be clear for the next several months, and I need a hobby that doesn't include exposing myself to the 'great outdoors'. I'll need access to the computers on the Daedalus oh…and Zalenka."

"It'll take us five days to get back to the Alpha site and then back here. But we can't just go into orbit and stay here, doctor. The Alpha site doesn't have any long-range sensors. If the wraith take an interest in the planet they have no way of knowing until they are almost on top of them."

"Thank you for that update on the situation, Colonel. I had forgotten all of that." McKay snapped.

"Rodney." Elizabeth rejoined the conversation with a stern tone. "I have to agree with you that we need to determine if John is alive and that you should concentrate on penetrating the shields. Unfortunately I also have to agree with the colonel. We are something of a sitting duck here. We know that the shields will keep the wraith off, but becoming besieged is why the Ancients left the Pegasus Galaxy. We don't want a repeat."

"So what do we do, just leave John there and sit back and play space invaders while the colonel shuttles back and forth between here and the Alpha site on the off chance that the wraith visit a planet that they completely culled two years ago? Where, if the pilots are not too busy watching their Top Gun DVD or doing their nails, they could be taking the jumpers out to act as an early warning system that should allow the Daedalus time to reach the Alpha site if necessary in good time to fight them off."

"Rodney-" Elizabeth began.

"No, Elizabeth!" McKay insisted. He realized as he heard himself talking that he had perhaps pushed himself a little too far, but he couldn't stop. "This is important. This is John we're talking about. A couple cases of MREs and some emergency cookies and some water in a tank on the twelfth level aren't going to do him much good if he can't get to them. He hasn't tried to contact us. Not by so much as a post-it on the outside of the tower. He was sick, and.and someone must have done something to keep him there. You have to let me do what I can-." Ronon was behind him again, one hand on his shoulder, forcing him down onto his improvised chair. He took the microphone out of McKay's hand.

"He's tired and he wants to help Sheppard. So do I. Why can't the jumpers run a watch there and the Daedalus switches her schedule around so that there is more time here and less there. That should give McKay time to work on whatever it is he needs to and still gives you coverage there. By the time the ship gets back with Zalenka he'll be rested and have a plan."

"A very good idea Ronon." Elizabeth agreed. They could hear the concern in her voice. "We'll be asking some questions here, and hopefully have some answers by the time we can contact you again. Rodney, you have to take care of yourself. You are still recovering from the flu, and if anyone is going to be able to solve this problem it is going to be you. You have to have faith in John. You know he'll do everything he can to survive. That's just he way he is. He knows we'll be trying to reach him."

"I agree." Caldwell chimed in. "Sheppard is good at survival. He's proved that often enough. You'll have all the resources at our disposal doctor, when we return with Dr Zalenka. I'll see if I can't persuade Hermiod to find another gear and get us back faster." He paused. "I'm told your supplies have been transferred. We're breaking orbit now and heading back to the Alpha site unless there is something else you need now. The sooner we go the sooner we get back." McKay shook his head, weakly waving a hand. Ronon took that to mean he had nothing further.

"We don't need anything else for now. Atlantis Mainland out." Ronon signed off and set the microphone down. He looked at McKay slumped on the boxes. "When did you eat last?" The scientist shrugged. Ronon guided him to his feet and over to his mattress and sat him down. He then went out of the hut and returned a few minutes later with a steaming bowl of something that filled the hut with a very good smell. McKay who had not moved sniffed and looked around.

"The doc is a pretty good cook. He made some soup and bread. Eat this and then you're going to sleep. You can't help Sheppard if you aren't thinking right." McKay started to protest, but then found his hands full of a soup bowl and a hunk of bread. The smells almost overwhelmed him, and he nodded in compliance. Maybe just a light dinner and a short nap, and he could get back to saving Sheppard.

Chapter 9-

John Sheppard was pretty sure that he wasn't dreaming. At least if he was it was a little more realistic this time as he seemed to be lying in his nest, blankets bundled around him and his breath visible in the cold air. He was lying on his side with only his face exposed to the chill of the room, and it took him several minutes to realize that he was staring at an empty Tylenol bottle, two empty bottles of water, five power bar wrappers and a large pile of MRE containers, also empty. He didn't recall taking, drinking, or eating any of the above.

He struggled out of the blankets, and pulled himself to a seated position, his head barely clearing the overhead table. The lights in the room brightened slightly as he did so. A cough tickled at the back of his throat, and he could not contain it, but he was pleased to note that it had less of the croup quality it had before, and his chest didn't hurt as much as it had, nor did he have any mucus. Evidently the flu and pneumonia was passing.

He looked at his watch, and could feel his jaw dropping. He had been asleep, or unconscious, for just over ten days! He pushed a hand through his hair, and grimaced at the greasy feel of it. He felt dirty all over as a matter of fact, and was glad that he couldn't really smell himself. He managed to push himself to his feet, and stood swaying in place for a moment as he waited for the head rush to pass. His eyes fell again to the wrappers and bottles, and he looked toward the bathroom facilities that were nearby. He had obviously fed himself and gotten water and had at least answered the call of nature as he hadn't…Well he hadn't disgraced himself completely by wetting the bed. He just didn't remember doing any of it. Shaking off that thought for another time, he went in to use the facilities. He was starting back out when he caught sight of his reflection in the mirror. At first he just grimaced at the rumpled picture he made, but then he met his own eyes in the mirror, and suddenly his 'dreams' came flooding back to him.

He staggered back from the mirror, eyes wide and frightened, and rushed out of the room. He moved to stand in the middle of his new domain, carefully studying everything in the room, looking for proof that it had all just been a dream brought on by the fever and exhaustion and stress of the flu and his situation. He could see nothing that either confirmed or disproved it. That meant it was just a dream right?

"Why do you fight so hard to deny what and who you are, John?" A voice asked. A voice he recognized not only from his dream, a voice that came from not only all around him, but also from within him. Crap, he was still dreaming.

"No John. You are not dreaming now, and if you recall, we told you that you were not really dreaming before, though your mind categorized it as such."

His mind reeled, trying to remember what had happened, what had been said. He recalled her, them, the woman who looked like his mother. Who had felt like…No, not going there. He remembered the groups of ancients, evacuating the city, the familiar man at the consol, the running, and the talking on the pier. Everything came flooding back to him. It had seemed real. But it had been ten days, and he had been, still was evidently, sick.

"You have been very ill. Thankfully enough systems were restarted to help you take care of yourself, as we were unable to aid you directly. Had the link not been established we would have been forced to watch as you suffered and been unable to do even what we did."

"What exactly did you do?" he asked uncomfortably. He tried to remember anything beyond the dream, beyond the darkness that had pulled him down, but nothing came.

"We made sure that you woke sufficiently to care of yourself. You ate, drank, and took care of your bodily functions. We also made sure that you took the medications that you had found, though we did not feel that they were sufficient. However as we had no access to our chemical database or to supplies to create the proper medicines, we had to allow you to take what was at hand."

"And I don't remember any of that because…?" He was beginning to feel angry, angry and violated.

"You were very ill. Your body temperature rose to over 40 ferats, 105 of your degrees Fahrenheit. You were sometimes delirious for days on end. You needed fluids and medication to suppress the fever, and food to give you strength to fight."

"And you made sure I got that exactly how?" He wanted a full explanation, for everything, but he wasn't sure exactly what to ask, so this line of questioning was going to have to do.

"Through the joining, we made the suggestion to your subconscious, and your body carried it out. Your conscious mind was…offline." Oh this was good. The disembodied voice was talking down to him now.

"So you manipulated me, like a puppet." He didn't do a good job of keeping the anger out of his voice he knew, but the very idea of some…thing having control of him like that was not making him happy.

"It was for your own good. We could not aid you directly, so this was the only option."

"You invaded my mind, 'for my own good' and you expect me to just say thanks and forget about it?"

"You are upset. We do not understand." He was pacing now as the calm voice echoed around him. As he reached a wall and went to turn, he slammed a hand into it.

"Stay the hell out of my head. Do you understand that?" He bellowed, feeling slightly foolish to be standing in an empty room yelling at the top of his lungs. There was a pause.

"We do not understand." This time the voice came from behind him, and he whirled to find himself standing face to face with the image of his mother, as she had been when he last saw her when he was eight. The anger grew.

"Stop doing that! You are not her! Stop looking like her!" He glared at the figure before him.

"We chose this visage because it is significant to you. As she was to you so are we now. It is…appropriate. So it has always been."

"YOU ARE NOT MY MOTHER!" He was in her face and in full angry mode with that little revelation. So he had a few mommy issues, it wasn't fair of them to take advantage of it this way. The figure did not so much as flinch.

"We are not your biological mother it is true, but as we are the mother of all who came before you, we are the mother of you now. You are the last of our line. We will do whatever is necessary to assure your continuation."

"And what if I don't want-" He cut himself off, realizing as he spoke that he couldn't exactly say he didn't want to 'continue'. He decided to redirect the thought. "What if I don't want you in my head?" The figure, he would not think of her as his mother, raised a hand and cupped his cheek, a gesture that he was ashamed to say he enjoyed for a moment before he backed away.

"We are not 'in your head', John. Your thoughts are your own, unless you wish to share them with us. You were ill, and your conscious mind could not function correctly. We simply gave your subconscious the direction it needed. If you had not wished to follow the direction, you would not have done so. We cannot control you."

"Yeah, so you say. How am I supposed to know that?"

"Why would we seek to harm you now? If we had wanted to do so, you have been here almost three years and we could have done so before. We would not have even had to take active steps we could have simply withheld our aid. During the storm, when the strangers sought to take us over, certain doors could have not opened when they did, or perhaps the shield might have been delayed a few moments more. Or when your people accessed the nanovirus laboratory on level 6, and you caused the EMP blast above us, had we wished you dead, the ship could have been told not to operate, and your people would have simply believed that you did not survive the blast."

He was forced to concede that particular argument. He had been aware of her, them, during the siege, had known that the city had been more responsive, had almost acted before he asked, as if anticipating his needs. He felt himself swaying slightly, and she was instantly by his side, pointing toward the bed.

"You must rest. Our scans are limited now, but they indicate that while the illness in your lungs has passed, your body is still weak. You need to eat and drink, and sleep some more."

"I just slept for 10 days…Oh crap!" It had just struck him that he had now been here for almost 12 days and the people on the mainland must be wondering where the hell he had gone. Ronon would be going nuts. And the Daedalus, it should have been here almost 9 days ago. That meant that Elizabeth and the rest of his team would know he was missing. They would be worried about him. Then there was the fact that someone; someone on the Alpha site now, had left him here. Whatever was behind that could mean danger for the entire expedition. He had to get a message out somehow. He turned away from the avatar.

"I have to get a message out to my friends on the mainland. Is there any way to send a radio message?" He asked turning to face her. She shook her head.

"That system is non-essential. It is not scheduled for restart for another 60 days. Even to aid you we can not change the sequence of the restart." She said it regretfully, and he believed her. He cursed, and forced his shaky knees to let him pace. He thought better of that when he moved.

"Then there has to be another way. They would have tried to come here, to see if I was okay. Can you tell me if they have?" She seemed to concentrate.

"We have no sensors currently engaged which would give us that information. Proximity sensors will not be engaged for another 10 days 5 hours and thirteen minutes."

"That's not particularly helpful." He snarled, his concern pushing him. This had to be some kind of plan against the expedition. What if they had wanted him out of the way for some reason while they went after his friends? They would have 90 days to do whatever they wanted to do. They might be after Rodney, or Elizabeth, or all of the scientists. Why they had chosen to isolate him was a puzzle. He was only one man, and his remaining men: Lorne and the marines, they would protect the scientists with their lives if necessary. Removing him would not change that.

In order to warn them however, he had to make contact with the outside. He was sure that by now Rodney knew he was missing from the mainland. He would be trying to figure out how to get through the shield or at the least communicate. He had to think outside the box or in this case outside the city. At this point, from Rodney's point of view, he was like Schrödinger's cat, neither alive or dead, but instead somewhere in between. McKay couldn't prove conclusively one way or the other that he was alive or dead. It must be driving the scientist nuts. With a quick smile at that thought he spun around and looked at the avatar again.

"I need a place on the city that comes closest to the shield, somewhere I can get to, where I can leave a message of some sort. So that my friends will know I'm alive."

"We are unable to project a schematic of the city at this time. That system-"

"Yeah, yeah, I get it. It's non-essential and won't be up for a specific amount of time that I am sure you can quote to the nanosecond. Stop telling me what you can't do and tell me what you can do." She stared at him for a moment in a calculating way that made him slightly nervous. Then she smiled.

"We cannot project the schematics, but if you will open to the joining, you will be able to access them yourself."

"Open…?" He didn't like the sound of that.

"You feel the joining within you. You always have felt it to some degree, but you are fighting the new deeper joining. You are frightened of it."

"I'm not frightened." He snapped, running his hands through his hair. He scowled at the feel of his greasy hair again. After he figured out how to contact the outside, next on the list was a bath. He paced some more. All right, maybe she, they, were right. He had felt a connection with the city since the beginning, but it wasn't something he contemplated. When it had gone, before when the system had completely shut down, he had missed it. Now, as the system started the long process of regaining its usual status, he could feel it again, but with a difference. Where before it had tingled in the base of his skull, now it skittered along every nerve in his body like an electric charge. And it was right about the other thing too, it frightened him. But what was his fright compared to his friends' safety? If he could find a way to communicate by…opening to the joining, then he had to do it. He turned to face her, and looked into her eyes. She read his acceptance and smiled.

"Think about where you are in the city, John." She said, and he had to smile as he remembered the directions he had gotten three year ago from Rodney McKay. Then he did as she said. He was vaguely aware of falling to his knees, but could not be bothered about it as his mind suddenly was overwhelmed by the influx of information. It was like getting a sip from a garden hose, then suddenly having it turn into a fire hose.

He lost himself in the sheer volume of data for several minutes, until he learned how to put on the breaks. The flow stopped, and he knelt there for several minutes breathing hard. He had closed his eyes but as he regained his equilibrium he realized that he could still see. But he was seeing not the room he was in, but instead a portion of what he understood was a schematic of Atlantis. Reaching out mentally he grappled with the schematic until there was a 3D representation in his head. A small dot, a mental 'you are here', appeared at a point near the gate room. At another thought a shield formed around the schematic. He was looking at Atlantis as it was now.

He mentally looked over the model, looking for the right place. The shield was nearly transparent, so if he could find the right place…He thought about what he wanted, and the schematic changed, the first place wasn't right, he could not access it easily. The picture changed, that one too wasn't right. He scanned and discarded several more before he found the one he needed. It was a balcony, on the fourth level near the west pier. It would take some walking, and he would have to haul any supplies he would need out there manually. The question was, would Rodney see it, and when? Had they already come? Would they come again? His team would not give up. He had to believe that. They would not just leave him here alone. He mentally shut down the schematic and opened his eyes. The avatar stood before him smiling.

"You have learned quickly. We are pleased. The joining is proceeding beyond expectations. We feared that due to your different physiology it would be difficult for you, but your blood is strong. Neelam had one of the closest joinings to us we had ever known."

"Who's Neelam?" Sheppard asked as he pushed himself to his feet. He was swaying a bit more now. It looked like he was going to have delay that hike until he could get a bit more sleep after all. He stumbled to his bed and sat.

"Neelam is the man you saw in the gate room when we showed you the leaving. He was dressed in brown and stood talking with the council. They valued his input, as your council values yours. He would be proud of you."

"Why would he be..." The coin dropped. "So you're saying that this Neelam guy was my great, great, great, ad nausea, grandpa or something?"

"Yes. He is your ancestor. His blood sings in you, it calls to us across the millennia. We cannot tell you the joy we felt when first we felt your presence. Had you not been in the vanguard of those who came through the ring we would have been forced to terminate them." He felt a chill at that bald pronouncement. He thought about how he had almost said no, about how his inclusion in the expedition had been an accident to begin with. If he hadn't been there, would anyone have been allowed to stay? Would Elizabeth and the others be dead?

"What about Beckett, and Kusanagi, and the others with the gene, the bloodline. Would they have been enough?"

"Their blood does not call to us as yours does. Both of your biological parents were of the line of Neelam. This made it stronger in you. You are the strongest of those that remain. We welcome the others however, their offspring will know a portion of the joining you now feel."

"And the people that have had the gene therapy? How do you view them?"

"This practice is not unknown to us. Those who have had the treatment are accepted since it is from your blood that they are endowed. They cannot know the joining, but their offspring may." Sheppard's head was starting to spin, though he wasn't sure if it was from the conversation, or from the data transfer. He lay down and pulled the blankets back up around him. The avatar bent over him and raised a hand to his cheek. He realized that it didn't quite touch him, as it had in the dreams, but he felt a strange warmth gather there. The warmth moved over his cheek and down his jaw, like the stroking of a hand. He felt sleep calling him, and he sank into it. When he woke, he would contact his friends.

Chapter 10-

Rodney had gotten his meal and his nap. In fact the nap had ended up being almost a full day. He had raged at Ronon about the amount of time wasted, but the Satedan had shrugged and wondered off. Evidently the other pilot, Goren, had been out to the city earlier that day, and found nothing. McKay had had some more food, and had started laying out what he wanted to do when the Daedalus got back. He also kept up his search of the schematics, looking for weaknesses, and places to search. He was building a list of areas to check each day, though he knew that the longer they went with nothing, the more likely it was that Sheppard was…well, incapacitated. He ignored that thought as he concentrated on his work over the next weeks.

It had now been over fifteen days since the city had sunk. The Daedalus had returned bearing not only Zalenka but also Teyla, Carson, and Elizabeth. Lorne was in charge back at the Alpha site. With the arrival of the great ship Rodney's computer power had gone up, but there had been no results. Between the three of them, he, Zalenka, and Hermiod had pretty well covered three languages worth of curse words, and most of the schematics of Atlantis. The possible areas of contact had been numbered and mapped and were visited daily by either Rodney, Carson or Goren. So far there had been nothing.

It was McKay's turn to take the jumper down and do the rounds of the contact points. He hoped that Sheppard appreciated the fact that he was not only in a jumper that was under the water without complaining, but was actually piloting it. The fact that he seemed to keep drifting off course was between him and the jumper. He was pretty sure however that Ronon and Teyla knew when he had veered off course, though they didn't say anything. He was simply glad that they had come along. He would never admit it, but he was lonely. He hadn't realized just how much he depended on Sheppard for his off duty entertainment. He was really going to have to get a life, once they got Sheppard back of course.

He guided the jumper around the curve of the shield, almost on autopilot, and was so surprised at what was revealed that he almost steered the ship into the shield. He heard Teyla's indrawn breath from the co-pilot's seat, and Ronon was pushing forward to see.

There, on one of the balconies near the western pier, in the place closest to the shield, were three words, glowing in the dimness of the depths.

"I'm still here." Rodney read out loud. He was pretty sure Teyla could read it, she had been studying the language for the last several years, but Ronon had not. "It say's 'I'm still here'! That wasn't there yesterday. Not even that sheepherder Beckett could have missed that." He turned a megawatt smile on his teammates, and had it returned. "He's alive!" Teyla jumped up and hugged them both, and they hovered there simply staring at the words for endless moments before McKay suddenly remembered that they were not the only ones waiting for such news. He activated his radio.

"He's alive! Elizabeth, Zalenka, Beckett, he's alive!" He announced on the open channel.

"Oh, thank God!" That was Elizabeth.

"Where are you, Rodney?" Zalenka.

"Can you see how he is?" Beckett.

"We can't see him. We're at point…W1, the west pier balcony. He's fixed some kind of glowing letters, It's gotta be those phosphorous sticks, the chemical lights. He's spelled out 'I'm still here'. We can see it plain as day." If his voice sounded ever so slightly choked up he put it down to too many hours of work and not enough fluids.

"Is there any way we can let him know we saw the message? That you can let him know you are there?" Elizabeth asked.

"Use a drone." Zalenka suggested.

"Are you daft man? We just found out he's alive, and you want to go firing explosives at him."

"Would only need to use low yield. Would be like knocking on door. Shield has been made to take much worse punishment. Would get his attention, no?"

"Would get his attention, yes." McKay said happily, though kind of peeved that he hadn't thought of it himself, not that he wouldn't have sooner or later. He threw himself back in the pilot's seat and backed the jumper away. He concentrated on the weapons array, and made the necessary adjustments in the yield. He then fired it at the shield.

The drone sped forward and hit the shield in a flash of gold. The glow spread over the surface of the shield like paint on a wall for a moment, then faded. Moments later the compression wave rocked the jumper sharply. Once the last wave had passed he maneuvered it back toward the city, right in front of the place the letters still glowed.

"Do you think he is nearby?" Teyla asked. McKay shook his head.

"He wouldn't be out this far. The further he is from the edge of the shield the warmer it is going to be, comparatively. Out here it is probably damn near freezing. He's probably in one of the inner rooms of the tower. That's about the center of the city, and with no windows it'll be easiest to keep warm in."

"He doesn't have any heat at all? The water here is freezing cold."

'The computers don't need any heat to operate. In fact they do better in the cold. It was one of the first non-essential systems to go. The only heat he's going to have is body heat and whatever he can scrounge up, like a camp stove."

"Can't he burn something for a fire?"

"Oh yes, there's a good idea. He can start burning all the paper in the place, oh wait, we use computers so no paper. Well maybe the furniture, no, that's made out of composites that are made not to burn. Guess that leaves…nothing. Not to mention the dangers of carbon monoxide and smoke inhalation in a closed environment. He'll have to forego the pleasures of an open fire in the gate room." Rodney sniped. Ronon rolled his eyes. Teyla stepped in to sooth the argument she could hear coming.

"I was wondering how long it might take him to get here. If, as you say, he is in the central tower, he will have to walk or run to reach this point. If he walks it could take an hour."

"He can run it in fifteen minutes, if he's healthy." Ronon said. And wasn't that a question in all of their minds.

"We'll just wait here. It's not like he could have slept through that. If he was sleeping that is."

"Keep us posted, Rodney" Elizabeth ordered. "Colonel Caldwell is moving the Daedalus into geosynchronous orbit in case there is something we can do from here.

"Unless Zalenka has solved the shield issue, I don't know what that would be, but we'll let you know as soon as we see him. McKay out."

They settled down to wait. McKay sat in the pilot's chair, idly pulling up HUD readings, trying to penetrate the shield. As always, he felt like an interloper in the seat, as if it was meant for someone else, and he was well aware of who that someone was. Ronon and Teyla spoke quietly, but they all kept an eye on the balcony doors that they could barely make out through the distortion in the shield. It was almost forty-five minutes later, and McKay was getting decidedly nervous when Ronon jerked his chin toward the balcony.

"Something's happening." The doors had opened. It seemed like forever before a red clad figure stepped through onto the balcony, and stood looking out at them through the distortion of the shield. McKay almost unconsciously moved the jumper as close as it could get. The figure moved toward the rails. As he approached they were able to make out more detail.

Sheppard was clad in what McKay realized had to be his cold weather gear from Antarctica. A complete suit of highly insulated materials comprising a set of pants, a parka and gloves. The only part of Sheppard that was visible was his face. As he neared they could see that he had not shaved, and his beard, always heavy, was already covering much of his lower face. When he reached the rail he pushed the hood down on the parka, and the familiar shock of dark hair, messier than usual, was revealed.

It had been only fifteen days, and the beard hid a lot of detail, as did the distortion of the shield, but they could see that his face was thinner than it had been, and paler. He had obviously not been well, and probably still wasn't from the looks of him. Despite that, he was grinning like an idiot, and he lifted a hand in a jaunty half wave, half salute.

"Is there anyway we can speak to him?" Teyla asked anxiously.

"No, our communications are blocked." McKay said, thinking furiously as he waved back. He knew that Sheppard could probably not see them really clearly either, but he would know they were there, and he would be able to tell their general outline. That should be enough for identification. One tall guy, one short woman, and a genius, that equals team.

"What about code?" Ronon suggested.

"No communications. Did I mention that?"

"Use the lights." McKay scowled at him. What was this, 'steal McKay's thunder' day? He would have thought of that. He flicked on the outer light, and then turned it off. He then started spelling out his own name. Sheppard nodded and gave them a little finger wave. Great, the man could be sarcastic with a gesture. He spelled out a question. As soon as he finished Sheppard moved over to the glowing letters, and started rearranging them. He spelled out one word and stepped back. McKay rolled his eyes.

"I asked him how he was. I should have known not to waste the battery power." He snorted, as he looked at the word 'fine' spelled out in glowing sticks. He asked another question. This time Sheppard seemed to be thinking about his answer and then he started moving the sticks again, and breaking open some new ones. He had a limited space, and a finite amount of sticks, so he was obviously working on being as concise as possible.

"Lrd lab geek stnd Mrgrvs." Was what he spelled out.

"Lured to the lab. A geek st…, stunned him. I don't know what the last is. That isn't a word." McKay interpreted. So that explained why Sheppard hadn't gotten off the city, someone in the labs had stunned him. He looked at the words again, trying to understand the last word.

"He has dropped the vowels out has he not? If you put in the vowels, could you not get a name from that?" Teyla suggested. She did not take her eyes off John who was standing there watching them, obviously waiting for them to signal again. She could not imagine how he must feel, left all alone with only the prospect of more of the same for another two and a half months. She reached for her radio.

"Daedalus, this is jumper 3. We can see the colonel. He looks thin, but he seems to be all right. We are communicating with him via code. He says that a scientist stunned him. Do you have a list of the names of the scientist that were on Atlantis at the last?"

"We have a list jumper 3. There were seven scientists: Zalenka, Mueller, Ichimori, Dunstan, Mohammad, and Margraves."

"Margraves! That fits." McKay blurted. "He's a British national. Supposedly an expert on integrating our technology with the Ancient's. He stunned Sheppard and left him there."

"We'll contact the Alpha site immediately, Doctor." Caldwell said. "I'll have Lorne secure him and start asking some questions."

"Rodney, Teyla said he looked thin. Did you ask how he was?" Carson asked.

"Yes, Carson, and of course he answered like he always does. If you can draw a conclusion from that, I will bow to your medical voodoo."

"So he's 'fine' is he? Daft bugger. Even eating emergency biscuits and drinking water in a cold environment he shouldn't have lost noticeable weight in this amount of time. I'll bet you his flu turned into pneumonia. He's lucky to be walking around at this point if he weathered that alone." Carson didn't want to think about John Sheppard down there all alone in the cold echoing emptiness of Atlantis, sick and lonely.

"Well he is walking, and seems to be thinking okay. It would be typical of him to get the worst of it though. Is there anything you want me to ask him?"

"Ask about the food, and make sure he's drinking enough water. Dehydration is probably almost as bad as malnutrition at this point." The doctor suggested. McKay flashed the lights. Even through the distortion he could see the scowl on the bearded face and the brush off hand gesture. Sheppard played with the sticks.

"Too many mothers already. Atlantis taking care" Rodney read, interpreting the abbreviations. "What the hell does that mean? How many mothers does he have?" He didn't miss the fact that Sheppard hadn't really answered the question. He was distracted from it though when he saw that Sheppard was moving the sticks again. "What about Margraves? He wants to know about Margraves." He directed the last to the people on the Daedalus.

"We're on with the Alpha site now, Rodney. It's not as if he were just standing there waiting to be questioned. They are searching for him. Tell John we're looking into it." Elizabeth said. McKay huffed. He wasn't happy with the answer, and he was sure Sheppard wouldn't be either. He flashed the code. Sheppard punched the wall in frustration. He moved the sticks again.

"He says…plot…something…needisolate. Well that makes sense. He thinks Margraves is plotting something. What was his first hint? Thank you Colonel Obvious". He flashed the last at Sheppard, and received a slightly murky flip off in return.

"Didn't need a word for that." Ronon said in amusement. Then he frowned as he looked out at his team leader. "He's cold. He needs to get inside or something." About to protest that they had just gotten there, McKay really looked at the man, and saw what the Satedan meant. Sheppard had taken off his gloves to be able to move the sticks easily, and had left the hood of the parka down. After making his gesture Sheppard had tucked his hand back under his armpit, and was dancing from foot to foot slightly in an obvious effort to keep warm. McKay reached for the switch.

"I'm telling him we'll be back in six hours with an update. That should give Lorne time enough to search out Margraves and find out what the hell he was doing and why. I don't want to go any shorter or the idiot will wait out here until we come back." He explained to his teammates and the people listening on the radio. He saw Sheppard give another smack to the wall in frustration, but then he nodded. He moved to the light sticks again.

"Break his knees." Rodney read with a snort. "Not in a forgiving mood, I guess." He made an OK gesture. He and the others watched as Sheppard gave a halfhearted wave and went back inside. None of them wanted to admit how bad they felt watching the lone figure walk away from them. Once he was out of sight McKay headed the jumper back toward the surface. Once he had it in the air, he headed straight up into the atmosphere, and then into orbit. Minutes later they were docking with the Daedalus. It took them several minutes more to reach the bridge. Elizabeth and Caldwell were hovering over the communications area. As the three entered the communications tech straightened and nodded at Caldwell.

"Here's Major Lorne again, sir." He flipped some switches.

"Daedalus this is the Alpha site." Caldwell nodded to Elizabeth to go ahead.

"Go ahead, Alpha."

"I have good news and bad news, ma'am. We located Dr. Margraves and he's contained. The problem is that he's locked himself in one of the labs behind a force field and we can't get to him. Far as we can tell he has food and water in there and no need to come out until he wants to. I have Drs. Simpson and Kavenaugh working on getting him out. They are not optimistic. May I ask what the word is on the colonel?" Elizabeth frowned at the news and motioned Rodney toward the microphone.

"He's alive. But he's cold and alone and looks like hell. Tell Simpson and Kavenaugh to get off their asses and get that field down or they'll be sharing the sewage cleaning duties for the next year." Mc Kay threatened.

"Gotcha, Doc. I'm sure they'll find that inspiring." Lorne said doubtfully. "I asked around about Margraves. Seems he's kept to himself since he came in on the last load of scientists. No one can recall having spoken to him for more than a few minutes. I can't even find anyone who knows his first name."

"Kevin." McKay said absently, his mind racing. He ached to be back down with Sheppard, even though there was nothing he could do for his teammate. He also wanted to be on the Alpha site prying the traitor who had stranded Sheppard in the city out of the lab. His musings were interrupted by Zalenka's advent, muttering in Czech. Long acquaintance, and some understanding of the less polite words of the language, let Rodney know that the smaller man was severely pissed. He was carrying one of McKay's laptops.

"That man, he is the one! He is the Zmrd who set off the reboot. I have found his tracks, he thought he was clever, but he is Blby. Kavenaugh could have done better. When I get my hands on him I will kick his prdel back to Earth." He declared to the bridge at large, his face flushed with anger. McKay knew that few things angered the little Czech like sabotage, and incompetence on top of it was just insult to injury.

"So he started this whole thing?" Elizabeth asked. Zalenka nodded, shoving the laptop at McKay who took it and started scrolling through the data. They all considered what they had heard.

"He was after Sheppard all along." Ronon finally said, leaning back against the bulkhead. The others all turned and looked at him, except for McKay and Zalenka who were now arguing in low tones, for them, over something on the laptop.

"Why do you think so, Ronon?" Teyla asked with a raised eyebrow. Ronon felt a strange sense of pride that no one had discounted his theory outright.

"He's been here what, two months? No one knows him. So what's he been doing all this time? You," He jerked his chin at McKay, who scowled at him, "didn't know that this thing was there so he couldn't have come here to use it, so he must have been looking for a tool. And if he was looking that hard, he must have had a purpose. If he just wanted the city sunk he had that done. He could have just gone to the Alpha site and waited and we would have known nothing. If you hadn't been trying to get Sheppard out would you have even found his tracks?" He addressed the last to Zalenka whose scowl matched McKay's.

"Maybe not. I would not have looked in that system if I had not been trying to penetrate shield." Ronon shrugged.

"He could have gotten away clean. Did he volunteer to stay or did you assign him?"

"He asked to stay behind. He was concerned, he said, that the interface between our technology and the ancient technology would cause some sort of problem. He thought he could help if anything came up. He seemed…eager to help." Zalenka said bitterly. McKay was snapping his fingers, taking Ronon's theory and running with it.

"If he only wanted to sink the city he could have set a time delay on the protocol and left on the Daedalus. We would have been none the wiser and by the time we could contact earth again he could have been long gone. Instead, he stayed until the last because he knew Sheppard would be one of the last ones off the city, and it was his only chance at keeping him there."

"What would anyone possibly gain by stranding the colonel on the city for three months?" Teyla asked. "It is not as if they have kidnapped him. No one has access to him now, not us, and not them, whoever they are. It does not make sense."

"We need to talk to Margraves. He has the answers." Caldwell observed.

"Well to do that we need to get him out of the lab, which I can't do from here. Even I haven't figured out how to be two places at once." He left it unspoken that he was not leaving. He would not abandon Sheppard completely. He looked at Zalenka. "You go and do it. Those two idiots are probably too busy sniping at each other to get anything done. If we wait too long Simpson will simply bitch slap Kavenaugh and try to do it herself when he goes off whining to Lorne for protection. She's passable, but I would rather you were there. We're not getting anywhere here. The Daedalus can be there in just over two days; go." He ignored Caldwell's grunt, something he interpreted as some kind of comment on his not being consulted, but Rodney wasn't concerned with hurt feelings now. There was something niggling at the back of his mind, and he needed to let it grow, mature, into something he could grasp. He started back toward the jumper bay, clutching his laptop.

"We'll stay in touch with Sheppard and keep working on breaching the shield here. Maybe he'll be able to help us from inside. He should be able to tell us what systems are back online at least and we can chart the progress of the reboot." He noticed he had something of a parade going on behind him, and as they got to the hanger bay he spun around and looked at Carson and Elizabeth, and ignored Zalenka. "So are you going or staying?" He didn't bother to ask Teyla, he knew she was staying. Beckett stepped forward.

"If you'll wait five minutes I'll get my things. I'd feel better if I was close by, even if I can't do a physical exam, I can at least get a look at the colonel. I'll not be leaving him there alone with no one to take care of him." Something in the speech caused that niggle in the back of McKay's mind to twist, but it still wasn't solid enough to get a hold of. He transferred his look to Elizabeth as Beckett walked out of the hanger. Teyla slipped out behind him, evidently to get her stuff as well. Elizabeth watched them go then sighed.

"As much as I would like to stay here and give John whatever moral support my presence might give him, I think it would be best if I were back at the Alpha site. I would like to be present when Dr. Zalenka gets the shield down. If this was some sort of plan, we need to know who's behind it. I don't think this is a personal vendetta against John. It's not like he's Robinson Caruso, getting stranded for crimes against the established order."

"Yeah, well literary allusions aside, I think you are right. It's not personal. He has to be working for someone, the IOA, or maybe even the Trust. We're missing too many pieces to see the whole picture. You're probably right about going back though. The grunts will string the guy up by his…" He stopped and smiled at Elizabeth's raised eyebrow. "They might get a little over zealous in their questioning. You know how much they like Sheppard." He thought he covered that pretty well. He was sure that he didn't have to remind her that Sheppard was very popular with his men, and that they would be willing to go long way to get answers, maybe further than was strictly necessary. Elizabeth gave him that look that said that she knew exactly what he meant, and took Zalenka's arm and started drawing him toward the door.

"We'll have the Daedalus relay any information we get as soon as we have it. They should be back in range within five days. We should have something by then. I'm sure Dr Zalenka will have the force field down in no time. Let John know that we are thinking of him." She left, with the Czech in tow. Perhaps the last time they had been forced to interrogate someone was a little too fresh in her mind for comfort. Ronon smiled at him.

"Would almost be worth it to go back with them just to get my hands on the guy." The big man said.

"Somehow I think that your usefulness as an interrogator is something Elizabeth prefers to forget." McKay said. He knew she still hadn't forgiven herself for setting the Satedan on Kavenaugh, even though it was Kavenaugh, and nothing had happened anyway, the big wuss. "Anyway, I thought you wanted to be here for Sheppard." It really wasn't a question, more of a statement, which the ex-runner confirmed with a nod. He headed toward the jumper.

"You might make it through the shields yet." He said in that deadpan tone that McKay always took as a challenge. He tilted his chin, arrogantly.

"Of course I'll make it through, it's only matter of time. It's not as if I haven't spent the last three years concentrating on the exact opposite of the current problem. Can we say wraith, and replicators, and tsunamis, and solar flares? Keeping the damn thing impermeable has been my focus up to now, it's just a little different when we want the damn thing to let us in." He headed into the jumper himself to start his preflight list while they waited on the other two. The sooner they took off, the sooner the Daedalus could go, and the sooner they would have the answers that might help them figure out why this was happening.

As he worked his way through the list, McKay tried to ignore the little voice that was reminding him that even if they could get Margraves to talk, it wasn't going to help Sheppard. He still had over two months to wait before the city would rise again. Two months without the sound of another human voice, without being able to bathe properly, having to exist on short rations and in a cold made all the more biting due to its solitude. The printed list suddenly blurred, and he had to blink rapidly to clear his eyesight. Must be his allergies. This re-circulated ship's air was hell on his allergies. He went back to the list, determined to ignore it, and the little voice.

Chapter 11-

Two months. He had been alone for two months now. Sheppard crumpled the shiny metallic wrapper from his "lunch" of an emergency cookie. It was actually his breakfast, his lunch and his dinner. He had been rather put out to find that while he had been sick Atlantis had fed him three and four times a day trying to maintain his strength. Evidently he had inconveniently thrown up a good portion of it, but the city had kept trying. They were not programmed for medical care. (Why did he get a sudden flash of 'Hotel California' when the avatar had mentioned that?) This had severely depleted his supplies. He had ransacked the quarters, and had found several stashes of MREs and assorted other foods, but he had finally worked his way through it, leaving him with the survival bars.

He was well aware that his body was requiring a good deal more calories than usual to maintain his metabolism at its regular state due to the continual cold. It had gotten a good deal colder throughout the whole city as the last of the heat had been expended into the freezing waters of the ocean. Damn laws of thermodynamics. He was basically living in his kit from Antarctica now. He had ransacked the quarters for additional gear, but had little luck finding much that could supplement his own things. Those that he did find were ill fitting, or not the same quality, and so he used them only when he had to clean his own gear, which happened when he could no longer ignore the smell.

Bathing had been, and continued to be problematic. He had found, with the help of Atlantis, a flooded section of the city that he was using as a combination bath and laundry. The water lapped at the bottom of a section of stairs, circulating out through a breech in the wall further west in the section, leaving him with clean, if briny water. The water was just barely above freezing, and his absolutions were hurried and rough, and not in any way satisfying. He had brought the camp heater he had found in one of the scientists quarters down and used it to warm the area and to dry his clothes when he did his wash.

He was going to have to talk to Rodney about how the chemistry guys were evidently producing a rather large amount of sterno for the heater. He had found a twenty five-gallon barrel of it in the same quarters as the heater, and assumed that Dr. Mburu was ever so slightly sensitive to the slightly cooler temperatures of Atlantis. If he recalled correctly the woman was from Kenya, and did not have the gene. Storing that stuff in personal quarters could not be safe however. Surely there was some way to plug in a simple heater. It had been when he was pondering that very question when another aspect of his new connection with Atlantis was revealed to him.

He had been bending down to pick up the barrel as he thought about the value of a truly 'universal' adapter for personal electrical objects, and had almost fallen over it when a flood of information had fed into his brain. Just as with the schematic the avatar had shown him before, the closest he could find to describe it was like being in a fun house, and suddenly finding yourself in a room that spun around very rapidly, yet you were expected to read the complete text of War and Peace on the walls as you spun. The really weird part was, as he pushed himself back upright, he realized that he had 'read' it all. He knew exactly how to adapt an electrical device that drew 110 volts to work with the Atlantis system. It was like there was a blueprint in his head, showing him what had to be done, and how to do it.

He had slumped back against the wall, and had felt the faint electrical charge that tingled through his body when he made contact with the city beyond the regular walking and casual brushes against a wall or doorway. It hadn't surprised him to look up to see her standing in the doorway of the closet smiling at him. He still wasn't used to her appearance, but he had ceased to complain about it. He didn't like to admit to himself that even though he knew it wasn't his mother, seeing that smile once again was worth the heartache he felt when he looked into the hazel eyes of the avatar.

"Very good, John. You have begun to access the data files. We did not expect this for several more weeks given the physiological differences. Perhaps the immersion has served to hasten the connection. Since the power systems are restarting, the interface data was available to you. You will find that the data will stay with you for several days with some clarity. After that you may need to access the system again to refresh your memory. It will be simpler next time since the information has already been downloaded to you."

"You mean that all I have to do is think about something, and the information will be downloaded to my brain like that? How can I fly if every time I wonder about something I'm getting a head full of data stuffed in my memory? Hell, how can I walk down the friggin' hall way?" It wasn't that this wasn't cool, but he could see this interfering with his job in a big way, and he wasn't going to have that. "Turn it off." He demanded of her. She blinked at him in puzzlement.

"It is an inherent function of the joining. It cannot be separated from it. Just as you are part of Atlantis, we are part of you, as is the data. If you are worried about the physical effects, do not be so. This is not an unknown phenomenon. Even though it has been many millennia since an adult was joined, the original builders of our interface had a similar response at first. As they acclimatized it became less intrusive, and more instinctual. If we extrapolate from their experience, within the next month as the systems restart, you will become more comfortable with the interface."

It wasn't a promise, but it was evidently as close as he was going to get from the city. She, they, had no way of being sure that his human physiology would react the same way that the ancient's had all that time ago. Over the course of the next month and a half it had indeed become second nature to him. As each system restarted, he found himself with new information downloaded into his brain.

The initial power system, the one that had shared that little tidbit of info about the adapter, had also shared with him the mysteries of shield generation. That had been the first thing the power system had taken over when it restarted, replacing the emergency system that had run it during the start of the reboot. He had almost spilled the sterno onto the floor when the system's mechanical satisfaction at a completion of task shivered through him. It was like the feeling you got when you finished a test you had been studying for, and knew you had aced it. He had blinked in surprise, and had tentatively sent a 'what the hell?' query out to the city.

The power system had practically bounced around his brain like a puppy with a new chew toy. It had triumphantly announced its take over of the shielding responsibility, and had proceeded to present him with a quick mental tour of the shield system. He still didn't understand everything he had been shown, but he knew the information was there. Rodney was going to be green with envy.

After that as the power system took over job after job from the backup system it announced its steps, and when the second system to start, the main computers, started to come online, he had been woken from a deep sleep in the middle of the night with a happy greeting and a mental promenade through what amounted to the system BIOS. He had sleepily contemplated the possibility of a simply finding the off button and doing this again at a much later time, but he had sat through as much as he could and then had gone back to sleep. The next morning he had woken up with way more information about ancient computers in his head than he really had ever wanted. It was freaky. Of course, he had yet to share this all with those on the outside. He hadn't quite figured out how he was going to tell them about this, and he certainly wasn't going to try with a bunch of light sticks or the stupid scrolly board he had found.

When he had been awoken on his fifteenth day to the sound of something exploding against the shield, his first instinct had been that they were being attacked by the wraith. He had sprung from his nest, gun in hand, ready to fight, and had been incredibly shocked to find himself still in the murkily lit conference room, dressed in his long underwear, and alone. Atlantis had helpfully told him where the explosion had occurred, and as soon as he heard he knew that someone had seen his message.

He had put out the glow sticks before he had called it a night less than eight hours ago. His internal clock was all out of sync with actual time, so he had been out at the pier in what was the middle of the night for the others, but he was hoping that someone would come, and he was counting on it being early in the day rather than later. The glow sticks were good for twelve hours, and it had been just over ten when the explosion had occurred.

He had dressed hastily and had run all the way, slowly. He was not happy with the effort it had required or the fact that it had taken him so long to reach the balcony. However he had made it, and had went out to see a jumper hovering just outside the shield. He had felt tears well up in his eyes at the sight, and had forced himself to wave casually rather than throw himself at the rails and beg them to come closer. In the end he hadn't had to beg as the ship had moved as close as possible, and he had been able to make out the shapes of his team inside the cockpit. He had been forced to blink back more wetness when he had realized who it was. They were here! He wasn't alone anymore. Well, at least not in the larger sense.

He had managed to get his point across about Margraves, the bastard, but other than that he had mainly just been happy to see someone. The fact that it was his team was a bonus. He had been deeply disappointed when Rodney had signaled about the delay, and that they would be leaving. He was a big boy though, and had managed not to lie down on the floor and throw a tantrum, no matter how he felt. He had instead waited until he had gotten inside before he had slumped against the wall and wiped away the anomalous water that had somehow gotten on his face, condensation or something. The Avatar had appeared before him, looking concerned, but he had shrugged her off and noted the time, determined to be in place in exactly six hours. If that was all the contact he was going to get, he was going to make the most of it.

That had been over a month and a half ago, and they had settled down to a schedule. Once a day a jumper appeared outside the shield at 0900. Sometimes it was Rodney piloting, sometimes it was Goren, the Marine pilot. Always at least one of his team was along. He had quickly run through the light sticks that he had on hand, and had gotten tired of using up the flashlight batteries for Morse code. He had remembered about a month ago one of those scrolling sign boards that you saw at video stores and stock exchanges was hanging in the geology lab with 'Why did the geologist take his girlfriend to the quarry? He wanted to get a little boulder' scrolling across it.

He had located the keyboard after a search of the lab, and had hauled the whole thing out to the balcony. His newfound knowledge of electrical engineering, Pegasus style, allowed him to hook it up, with Atlantis managing to route just enough power there for him despite the state of the start up. When McKay had questioned it he had said he had set up a battery feed using a battery from one of the MALPs. McKay had not been shy about his surprise at the possibility that he had done such a thing, but Sheppard figured it was easier than trying to explain this whole…thing he had going with the city. In any event conversation was now a lot more convenient from his end. He didn't dwell on just how much he looked forward to each day's meeting.

Even if all anyone had to say was 'hey' at least there was someone there. McKay had asked him if he had found his 'Wilson' yet, and he had spent the rest of the day hunting down spray paint and making a reasonable facsimile of a volleyball with wild hair on the wall of the balcony. Seeing the grin on McKay's face, and the puzzlement on Teyla's, the next day had been reward enough, though when Elizabeth had appeared a week later she had given it one look and told him she hoped it was water soluble.

When questioned about his living conditions he had been pretty straightforward with the reality of his situation: cold, dark, and lonely. What more was there to say? He figured anything else would have sounded fake. He had neglected to tell them about his ration situation. He couldn't help it if they had gotten the impression that he had more than he actually did. It wasn't as if they could do anything about it, and he didn't want them worrying about it.

Carson's inquiries regarding his health he had outright stonewalled. The Scot had been practically beside himself when he had reluctantly admitted the pneumonia. There was no way he was going to mention the time he was unconscious, or the weight loss. The cursing in Gaelic had been instructional in any event even when sent via Morse code. The Avatar had helpfully provided him with a litany of Ancient curse words, which was just wrong coming from someone who looked like his mother. He had finally begged her to stop.

McKay had practically tied himself in knots trying to breech the shield. The avatar, who had monitored the conversation through her link with Sheppard, had given him the reasons each try would not work, none of which Sheppard passed on, knowing that it would be a red flag to the scientist. Rodney, being Rodney, was not prepared to say die however, and continued to take readings and run scenarios through his computers. Sheppard encouraged him each time, knowing it was expected of him. He didn't think it would be best for them to wonder why he was so sure that there was nothing to be done. Fatalism had never been his shtick, and he didn't want them wondering about his sanity. He was doing enough of that for everyone.

With one month to go, the systems were well on their way to starting to reach those that the ancients had considered "non-essential". He had woken that morning to have the lights flare to their full brightness. His wince of pain at the sudden change had caused an instant drop in intensity, and an apology in his mind. The system had then proceeded to share with him the intricacies of the lighting requirements in each sector of the city, and the schematics for what he was pretty sure was an innovative, at least to Earth, lighting panel that required only a fraction of the energy of anything they had currently. He had only swayed slightly as the information downloaded into his head and he felt almost none of the nausea that first download had engendered. He had asked the avatar just why the systems felt they needed to share, and she had smiled at him in that way he was coming to think of as indulgent.

"It has been so very long since a joining has taken place. While each system is part of the whole, each is also autonomous, and wishes to make itself known to you as they would have before. A child would not have been able to comprehend the information as you do, but the connection would have been made."

"So basically the systems are like a fairy godmother bringing gifts to the christening." He summarized. She got that distracted look that told him that the system was drawing on his own memories to understand the reference, a process that still made him slightly uncomfortable, and then she nodded.

"It would be an appropriate analogy, if fanciful. Though we assure you there is no evil godmother to gift you with a harmful curse. We hope that sometime you will believe us when we say we mean you and the others of your expedition no harm" Evidently they had 'read' the whole Sleeping Beauty scenario from his mind, and the trepidation he still felt at the two-way nature of the joining.

"Yeah well, past experience and all that. No offense meant."

"None taken. You are the result of your past experiences, and we would not alter you. We find you fascinating, John Sheppard. You are not like any of those who came before." He had squirmed nervously under her smile and had gotten up to do his morning PT and put some water on to heat. He might not have coffee, but there was still a little of the tea left, and it was one of his days to enjoy a cup. He was stretching it so that he could make it through the next month.

He had found himself a calendar and had hung it on his little fort, and had been marking the days off. He had faithfully written on it when each system had restarted, knowing that McKay would want to know. As he waited for his tea to brew up he marked off the current day. He had done his morning meeting with the jumper, and was back to his usual time wasting process. He had further ransacked the rooms looking for reading materials. He had ended up with a mix of things that ran the scale from porn to scientific journals. He had been surprised with what he had found where, and it had given him an insight into several people that he was not exactly comfortable with. And he hadn't been blushing over that one magazine. He had simply been flushed from the heat of his camp stove. The fact that a figure that looked like his mother had appeared in the room at the same time he had flipped to a particularly explicit photo. He hadn't even known people could bend that way. He had carefully replaced that particular magazine, and the other more…sensitive things back where he found them, but had kept the rest, and was reading his way through. He was trading off between fiction and non-fiction.

He had also taken the opportunity to explore the city, as he had never had the chance to do. Once the power system had gotten to the point where it would not be strained by his wonderings he had started making sojourns into the parts of the city he could reach in a day with no transporters. He had found some notebooks and was making careful notes of what he found, slipping in the information that the reviving systems gave him about what certain rooms were when he thought he could get away with it without setting off any alarms in anyone's mind. He really needed to decided just what he was going to say about all this. He was putting it off though until it became a little closer to the time when he would actually have to talk to someone.

In between his wonderings and the reading he was doing some PT. Running was something of an experience when you were basically running into the darkness with the light following you as you went. He had to count on there being nothing in his path that he couldn't avoid, though as things progressed Atlantis had helpfully provided him a sort of heads up display that was in his head as he ran. That had taken a little getting used to, but he had soon found that he could not only run in the near dark with confidence, he could do it with his eyes closed. Wouldn't that freak Ronon out?

He was disappointed to find that he was forced to keep his PT to a minimum however when his weight had started dropping faster than he had counted on. At this rate he was going to look like a concentration camp survivor by the time the city rose. He really did not want to have that conversation with Beckett, or Elizabeth, or his team, so he cut back to just the running and some yoga in the morning. He would give anything for a good sparring session.

He had briefly considered taking up fishing, and trying to catch some of the denizens of the lower levels, but first he had no bait beyond his precious emergency rations and secondly he wasn't sure which would be safe to eat. Atlantis had been unable to give him any information on the possible inhabitants of her flooded areas since that section of the database was one of the last to restart, along with medicine and agriculture. Evidently the Ancients had Rodney's contempt for the soft sciences.

In his ransacking he had found several hand held games, powered by batteries, and had become the current Atlantis champion of Tetris, soduku, and crossword. He wished he hadn't packed up his PSP so early. He could have used that. The systems were not far enough along yet to allow him to use the Playstation or TV in the rec room, along with the DVD player. He was sort of looking forward to that in about fifteen days. He would finally be able to watch all the 'Back to the Future' films without subtitles provided by a certain scientist, not to mention finally getting as much playtime as he wanted on the Playstation. He'd show those marines a Halo score.

His tea had brewed up while he was contemplating his afternoon schedule, and he poured it out of the small kettle into a cup. He let the fragrant steam curl around his face as he took a deep breath, both hands wrapped around the tin cup he was using. The half gloves he had appropriated from the marine barracks kept his hands mostly warm, but the heat was comforting in a way that few things were here at present. He had developed a very big appreciation for the people that he lived and worked with. While he would never be a 'people person' in the sense of touchy feely/social interaction, he certainly would be happy to see every one of his fellow expedition members, even Kavenaugh. This is what he had brought down to.

He was just finishing his tea when he felt the 'bloom' of a new system. He was suddenly almost painfully aware of everything about him. His clothes went from a comfortable warmth that he was only subliminally aware of to incredibly itchy and confining. He seemed to be able to feel each thread in his shirt. He almost was to the point where he was about to throw off his clothes despite the cold when his enhanced perception expanded to include the entire room. He could feel the residual heat from the camp stove like an inferno on one side and the cold of the city like a spear of ice through the other. Another shift, and he could feel the emptiness of the city, with his own small presence forming the only warm spot in the entire expanse. Yet another jump and now he felt the waters around the city, icy cold. Felt fish and a passing whale, felt it as his awareness passed over the downed jumper where Rodney McKay had almost died, where Griffin had died. Finally he felt the ocean's depth changing at the distant shore in one direction, and the incredibly deep chasms of the open ocean equidistant in the other. Then, with a suddenness that was like being slapped he was back in his own body, with his usual perception. The avatar stood before him.

"The internal and proximity sensors have initialized." She announced.

"No shit." He mumbled and fell back in the chair he had been sitting in. It took several minutes before he could convince his brain to calm down. He was pretty sure that a part of him was gibbering gently somewhere in the depths of his mind. He just wasn't made for this. He finally blinked at her, and ran a hand over his face.

"I don't imagine that I could convince you guys to warn a fellow before that happens." He asked, pushing out of the chair. If he concentrated he could still feel the increased perception. He had to pull his mind back from following the track of a whale as it went merrily along its course, unmindful of its impact. The avatar tilted her head and he sensed that she was 'interfacing' with whatever part of him was now part of the city. She looked faintly abashed.

"We apologize. Your sensitivity was unforeseen. Your spatial awareness is enhanced as compared to that of those who came before. The system's initialization should not have affected you in this manner. Even your ancestor was not so attuned."

"Great. I'm sure that wherever he is out there in ascension land grandpa is very proud." Sheppard snarked. The avatar cocked her head. The city was not big on sarcasm he had noticed. "Just…warn a guy next time would you." He asked. She nodded.

"There is a gate ship launching from the mainland. Estimated time of arrival is 10.56 minutes." She said. He looked at her in surprise. She raised an eyebrow at him, a habit she had gotten from him he thought. "Do you wish to see it?" He nodded with a slight hesitation. She blinked, and suddenly he was looking down on what he assumed was Lantea from a position in orbit. After a moment in which he barely had time to acclimate to the new perspective it zoomed in to give him a view of the mainland, then even further to a small craft moving out to sea. It was a jumper all right, heading towards Atlantis. He blinked and pushed the view aside, swaying slightly as his sight came back to the room.

"I've got to get out to get out to the balcony." He said and without waiting for a response ran out of the room. The transporters were still offline; they were not scheduled until the last minute. He was faster now than he had been at first however, so he should not be too far behind the jumper's arrival. As his feet carried him swiftly through the city his mind was racing ahead of them. What could have happened that they were sending a jumper out?

The Daedalus was either at the Alpha site or on it's way back. The mainland could have heard something from them he guessed if the ship was close enough. Could something have happened at the Alpha site? Had Margraves struck again? Did he have confederates that had made some kind of move? Had the wraith attacked? Too many questions and not enough answers. He sped up, grateful for the speed with which Atlantis lit the way and opened doors. He was three quarters of the way to the balcony when he felt the strike of the drone. "Okay, that was unpleasant" he thought as he staggered against the wall. He was going to have to tell them he had sensors now so they didn't do that again. He was pretty sure that if he was casual enough about it that McKay shouldn't ask too many questions.

In another five minutes he was going through the doors onto the balcony and was headed toward the keyboard and sign. He could see that it was McKay in the pilots seat of the jumper, and saw his head jerk up in surprise when he came to a stop at the rail. He obviously hadn't expected him so quickly. He waved. Instead of waving back McKay instantly started flashing the lights. As he started reading the code Sheppard realize that the scientist was alone in the jumper. That was unusual and as the words started forming in his head, he knew why. Crap, he had run out of time.

Chapter 12-

McKay had been sitting in the hut chewing a power bar when the message from the Daedalus had come through. The ship was still a day away from the planet, but Caldwell's concise tones had passed on the news, and he had acknowledged it absently. As he spoke things started falling into place, starting with that first communication with Sheppard almost two months before. "Too many mothers already. Atlantis taking care."

Zalenka, with the dogged determination that had made him the scientist that he was, had finally prevailed against Margraves. The force field that had been holding Lorne and the marines back had been dropped at long last, and they had stormed the lab while he had been napping, secure in his position. They had found a weapon and a suspicious pill that Margraves had struggled to reach when he had woken to Lorne's boot on his breastbone. The chemists were still analyzing the pill.

The man had been stubbornly silent at first, refusing to so much as acknowledge that he had done anything out of the ordinary. It had taken a side trip by the Daedalus to a point where it could communicate with Earth to find out who exactly Kevin Margraves was, and who he worked for. Quick but effective investigation into his background had shown that the Kevin Margraves that specialized in the compatibility of the two technologies had been found murdered in his hometown of Liverpool three months previously. His body had been identified four weeks ago by a fluke, though nothing had been sent through channels due to the backlog of work in the Liverpool morgue. It would have eventually made its way through channels, but with the usual strange twist of luck, the truth had come to light in a slightly weirder way.

The inquiry on Margraves had been sent out from the SGC and had reached the desk of a missing persons detective in Liverpool for a reason that no one quite understood. A morgue assistant, the boyfriend of the detective in question, had been absently reading through the papers sitting on his boyfriend's desk as he waited for him to go to lunch, and had recognized the name. Things had gotten quite a bit more interesting from there. The Daedalus had sent back photos and fingerprints on their now unknown prisoner, and rapid steps had been taken to identify him. Less than a day later they had their answer.

The man's name was Alan Capponi. He was a known agent of the Trust, and he was an expert on computer systems. No further information had been gained on the SGCs side by the time the Daedalus had returned to the Alpha site, but the investigation was continuing. Capponi, when faced with the knowledge that they knew who he was and who he worked for had been somewhat less confident in his silence. He had attempted suicide using his sheet, but the guards had stopped it before he succeeded. Repeated questioning, along with some judicious threats from just about everyone, had finally broken him down, and he had spilled the whole thing.

The trust had come into possession of some information that detailed just how the ancients had interfaced with their technology. It had been a detailed study of the mechanics of how an ancient was 'joined' to the technology practically from birth. It was evidently the practice among those living in the cities, like Atlantis, to turn over their children at an early age to crèches run by the AI in charge of the city. In effect the child became a ward of the city. As the child developed the AI formed a bond with the child that made the accessing of the city systems as natural as breathing. It was the ultimate case of nature versus nurture.

In digging further the Trust had found reference to 'joining' of adults to the technology so that they had a similar connection beyond what was possible by simply having the gene. The original builders of the technology must have gone through a similar process to hook themselves into it, but it had not been necessary for those that followed, until the ancients had abandoned Atlantis, an had to all intents and purposes dies out. Their descendants, the gene carriers, were not born in the city, or any of the smaller facilities, and had no nurtured link to the technology. Therein lay the plan.

The Trust scientists, Capponi being one of them, had theorized that if an adult gene carrier with a strong enough incidence of the gene was placed in a position to be present when an ancient facility was 'rebooted', isolated from outside influence, there was the possibility that he or she would be 'joined' to the technology in much the same way that a maturing child's brain would have been in the original cities. The problem was that it was just a theory until it could be tested. The two strongest gene carriers known were two of the hardest men to get at. Jack O'Neil was now the head of home planet security, and was very well guarded, despite his protests. Also, he was not regularly near any ancient facilities. If the planet was attacked he might go to the base in Antarctica but then it could not be rebooted, nor could he be isolated there. No, General O'Neil was not a good prospect.

At first consideration John Sheppard was an even worse choice. While his might be the strongest gene found to date, he was also the furthest away. He was well outside the Trust's usual stomping grounds, and protected from any but the most serious threats. However, when considered in the light of where he lived, he was ideal. Sheppard lived and worked in an ancient facility, one of the cities that had been spoken of in the report. No need to take him anywhere, to kidnap or lure. The problem became how to 'shut down' Atlantis. Evidently the Trust agents were very good at their job, as they had managed to get a rather large amount of information out of the SGC about the Atlantis system. Capponi had familiarized himself with the system, and had theorized, based on several references found in what amounted to work diaries, that a reboot function existed somewhere in the system, and had in fact been used before. It was only a matter of finding it. That had been the reason for his charade as Margraves. He had needed to be in the Atlantis system to track down the program, and after two months of looking pretty much around the clock, he had done so.

After that it had been a fairly simple matter of coming up with a plan, which had been surprisingly simple, and made all the simpler by Sheppard's decision to remain on the planet. Capponi had at first been prepared to remain on Atlantis himself in order to physically hold Sheppard there until it was too late, but circumstances had worked in his favor, and he had made his escape. When he had heard the rumor that contact had been made with Sheppard in the city he had known it was only a matter of time before he was implicated, and he had gone to his fall back plan. He had locked himself in the lab with the intention of remaining there until the 90 days were up and the plan completed. He had not planned to return to Earth alive in any event, but he had wanted to know the outcome of the experiment. Had Sheppard 'joined' with the city?

Evidently it was a question that was on everyone's mind right now. Caldwell had made sure that McKay understood that the SGC wanted to know exactly what was going on with Sheppard in the city. If the colonel reported ANY increased connectivity with the ancient technology the SGC was to be notified immediately, and once the city rose Sheppard was to return to Earth via the stargate, where he would be debriefed and tested. If he had become something more than just a gene carrier, he was going to become the darling of the scientist set. Rodney could practically hear the drool dripping from here.

He thought about the words he had read before again "Too many mothers already. Atlantis taking care." He thought about the scrolling sign that had appeared last month, supposedly hooked up to a MALP battery. He had seen Sheppard mess up replacing batteries in his PSP, and he was supposed to believe the man could rig a set up like that?

Next, Sheppard had also been able to give them a fairly detailed list of what systems were back online. While McKay was prepared to believe that Sheppard was observant enough to notice if the lights were brighter all of a sudden, there was little reason for him to know about the power inducement systems that he had mentioned the previous week. Rodney was pretty sure that there weren't five people on Atlantis who even knew what they were, and Sheppard was not one of them.

He had also noticed something else. When he had been describing his various plans for breaking through the shield he had noticed that occasionally Sheppard's attention would wonder away for a moment before he would answer. Invariably he would cheer Rodney on, saying he was sure the scientist knew what he was doing, yadda, yadda, yadda. He would make all the pep talky noises, and seemed to be optimistic about their chances. But it was all an act. Sheppard didn't just think he was stuck there for the entire time, he knew he was stuck. And it was more than simple resignation. John Sheppard wasn't stupid, despite anything that McKay might say to the contrary. He didn't understand the shields the way Rodney did however, yet he had been asking questions as if he did. Just last week Rodney had thrown out a suggestion regarding the shielding near underwater jumper bays, it had been more facetious than real, but Sheppard had come back with a question about pressure equalization and atmospheric differentials that could have come from a marine engineer. McKay had been so surprised by the question that he had almost missed the look that flashed over Sheppard's face, and the irritated glance he had thrown over his shoulder at what had appeared to be empty space.

Either Sheppard had been hiding more of his light under a bushel than he had revealed before, or someone, or something, that understood the question, and the difficulties inherent in the problem, was prompting him. McKay was willing to bet it was the latter. The problem he now had was two fold. First he had to prove it, and the only way to do that was to get Sheppard to admit it. Since he had ample proof that Sheppard would resist coercion to the death, be it physical, mental, or emotional, and the fact that he could not interact with the man except via code, persuading Sheppard to admit it was going to be difficult to say the least.

The second issue was what to do about it if Sheppard did admit it, and McKay had absolutely no doubt that Sheppard was now connected to the city in a way that had never before been contemplated by a modern human. All of his data supported the hypothesis. But what would happen once everyone knew? Yes, they could have access to all the data in Atlantis' vast storage. There was information there that they did not even know how to comprehend, much less theorize about, Rodney knew that, and he longed, almost with a physical ache, to access it. The secrets to the very workings of the universe might be in that database, locked away by their own ignorance. John Sheppard might be the key to that information.

But McKay knew how these things worked. If Sheppard were shown to be the ultimate key to Ancient technology, then he would be taken from Atlantis, and probably locked into a lab in area 51. He might be let out occasionally to activate remote facilities, maybe for the infrequent meet and greet with the Asgard or the Tollen, carefully guarded of course, but he would never be allowed to continue doing his job here in Atlantis, or live a normal life. Even if by some incredible feat of diplomatic finagling Elizabeth managed to keep him here in the Pegasus galaxy, he would not be allowed to leave the city, even for something as prosaic as a jumper ride to the mainland. He would be a prisoner of the city, and he would be constantly under the microscope of a brigade of scientists and psychologists and geneticists, all trying to study, understand, or duplicate him. They would destroy everything that made Sheppard what he was. They would take it all away from him. Rodney could not do that, not to Sheppard, not to his best friend. Not even for the secret of the universe. He crumpled the wrapper of the power bar in his hand and rose to his feet.

Five minutes later he was slipping into the jumper and closing the ramp. He walked rapidly to the front and sat down, already thinking the ship on. He was in the process of cutting short the checklist, a practice Sheppard would have reamed him out for, when he looked up and saw Ronon and Beckett standing in front of the jumper. When Beckett saw he was looking he hit his radio.

"Where are you going, Rodney?" he asked. McKay bit his lip. He knew he was crap at lying, even more so to his friends then to strangers. They knew him too well.

"I uhh…I have something I have to check at the city. I may have found an access port, but I have to check it in person. I'm just…just running out to take a quick reading and I'll be right back. Don't hold dinner." There, that didn't sound too bad did it?

"We'll go along with then." Beckett said with a smile that told Rodney that no, they hadn't bought it. "Lower the ramp." McKay started shaking his head, and rushed through the last of the absolutely necessary checks, multitasking for all he was worth.

"No, no. It's nothing you two need to come along for. Surely there must be more fish you can go and torment Carson. I'm sure Ronon would be happy to show you how to scare them out off the water, no worm needed. I'll just leave you to that. Be right back." He was on the final check now.

"Rodney-" The doctor started, only to stop and back up rapidly as the jumper started to hover. "Rodney what are you doing? What's going on?" At that point McKay turned off his radio and thought the jumper up and away. He tried not to think about what messages might be sent to the Daedalus and the Alpha site. He would have to do damage control on that later, for now he needed to talk to Sheppard.

Fifteen minutes later he was parked outside the shield, sitting in the pilot's seat, and staring at his hands as he waited for Sheppard to respond to the 'knock'. His mind was whirling with the possibilities. He was so torn. Half of him, okay 90 percent of him, the scientific part, was practically vibrating at the thought of the breakthroughs that could be made, the information that could be accessed, the things they could do. That part had no consideration for the cost of those revelations, for the man who would be lost to it. What was one life when all the secrets of the ancient's could be revealed? Think about the advances to science, medicine (no, it wasn't a science), to the very fabric of the lives of every living human. It could lead to the defeat of the Ori.

The other ten percent was practically hysterical with the thought of what it would do to Sheppard. It was raging at the other part, using words that were quite unnecessary and untrue, thank you very much. "All previous arguments regarding what it would do to Sheppard aside, the smaller part suggested to the gestalt, "think about what it would mean to US. Sheppard is one of our few friends. We do not have so many that we can afford to toss one under the 'for the good of science' bus just like that." The scientist was about to make a biting, and no doubt stunningly brilliant, reply when movement in front of the jumper drew McKay's attention from his own thoughts. He blinked in confusion as he realized that it had only been five minutes since he had 'knocked'. There was no reason that Sheppard should have been nearby. Another item was added to the list of proof. The scientist thumbed his nose at the smaller part, who sneered back. Good God, this whole thing was making him consider himself in multiples. Leave it to Sheppard. He reached for the lights button, ignoring Sheppard's wave.

It took him several minutes to get the explanation and his questions out, but since he had been formulating them since before he took off, it was only due to the constraints of having to do it one letter at a time. When he had finished he hesitated, then sent three letters…WTF.

Sheppard stood staring at the jumper for several minutes afterwards, and Rodney wished that the shield were transparent enough that he could read what was going on behind those changeable eyes. The face definitely didn't give anything away. He was about to start pushing when Sheppard turned abruptly away and started for the door. He was leaving? McKay fought down the urge to fire another drone at the shield, knowing that even at reduced yield his proximity would probably result in the destruction of the jumper. Instead he mentally nudged the jumper forward until it banged into the shield. The resulting noise must have been sufficient since Sheppard stopped abruptly just as he was marching through the doors. He stopped, but he didn't turn. Minutes passed. Finally, Sheppard's head dropped, and he turned and walked back out to the railing and the scrolling signboard. He was about to start typing when his head jerked up and around. McKay looked, but he could not see whatever it was that had drawn Sheppard's attention. He looked back at Sheppard.

The man was arguing with thin air! He had dropped the keyboard on the deck, and had moved back toward the doorway. As Rodney watched one hand came up in an almost pleading gesture, and then was waved in his direction. As he watched, fascinated, Sheppard continued arguing with nothing. After years of studying the man, McKay had no trouble seeing just when he went from pleading to demanding and from demanding to incendiary.

Sheppard's body language was usually completely deceptive. McKay had seen him go from relaxed to the point of seemingly nodding off one minute to erupting in volcanic rage the next. He had sometimes wished for some sort of translation device, a Rosetta Stone for understanding the man, but had come to realize just how complicated that would be. Maybe it was the isolation, maybe it was whatever had happened inside the sunken city, maybe it was something else altogether, but now there was no mistaking that Sheppard was completely incensed. He was waving his arms, and the tendons in his neck were taught from yelling. Whatever he was doing, he very definitely was not happy and he wasn't bothering to hide it. The argument seemed to be going on and on.

With a suddenness that startled him, Sheppard suddenly broke away from whatever he was arguing with, turned, and ran toward the rail. He made a sweeping gesture with his arm and seemed to be yelling at McKay. It was clear that Sheppard wanted him to go, and right now.

He was fumbling with the instruments, still awkward with it even after all the times he had done it, and had started to pull back when something slammed into the side of the jumper. He tried to hang on, to stay in his seat, but the small ship heeled over onto her side, and he was slammed into the wall. The ship continued to spin, and he caught sight of the city, moving upward, and he realized that he was sinking. He had only one moment to panic, his mind going back to another sunken jumper, before he slammed head first into the ceiling, and knew no more.

Chapter 13-

Sheppard heard himself screaming like a maniac as he ran toward the railing, trying to warn McKay away, trying to make him understand with only a gesture that he HAD to leave. But even as he made the move he knew it was too late. Seemingly out of nowhere a drone slammed into the jumper, flinging it on its side. He could see Rodney being tossed to the side, and could only gape as the machine tumbled over onto its top and began to sink. He spun on the avatar who stood in front of the doors.

"Damn you! Why did you do that? He was here to help me."

"He indicated that your leaders would remove you from the city if their hypothesis had proven true. Since it is true, that means that they would try to take you. This can not be permitted."

"And what if I had wanted to go?" he asked, one eye on her and one eye on the jumper that was slowly sinking. It was almost out of his sight now. The avatar looked stricken.

"You would leave us? We have become as one. You are the first in so many years, the last of our line." She almost looked like she was going to cry. He hardened his heart and slashed a hand through the air. The jumper was only a few lights shining through the darkness of the water beneath Atlantis.

"That's not the question. What if I wanted to leave? You've said that this…thing is voluntary on my part, that you can't control me, but you just made a decision for me, a decision I very definitely did not approve of." The lights were almost gone.

"We cannot control you. We speak only the truth to you. We can do nothing less. He was a threat and we moved to block it, to protect you. It is you who control, not us."

"He's my friend. And I don't need your protection, at least not from him. If you harm my friends you harm me." The lights were gone. He felt his stomach twist.

"We meant no harm to you. We cannot harm you." She was wringing her hands now in distress.

"Well you just did. We have to help him." He demanded.

"We have no means-" she started

"There has to be a way. Think!" he said. He closed his eyes and forced himself into the database. Schematics and plans flew through his mind faster than he could catalog them, his mind sorting and discarding what he could not use. He felt Atlantis guiding his thoughts in certain directions. He pushed harder, and harder still.

"You will do yourself injury, John." The avatar's voice rang through his head but he ignored it. What use was this joining if he couldn't use it to save his friend? Terabytes of data flew through his head in milliseconds, information buffeting him like a hot wind. He didn't even try to remember any of it. Then…there, there was something. He reached out and mentally grappled the schematics to him. It appeared around him as if he were part of the mechanism, and he felt the information filling him. This was it.

"Engage this system." He grated out, ignoring how his voice sounded. He was vaguely aware that he had fallen to his knees, but he ignored that too. He opened his eyes, having to blink several times to clear away the schematics. The avatar was shaking her head.

"That system is not scheduled to initiate for another thirteen days we cannot-"

"The fuck with your schedule. Initiate this system, NOW." He staggered to his feet, absently swiping at the moisture he felt under his nose and on his chin. She was still shaking her head.

"The protocol-"

"Fuck the protocol! It is not the most important thing here! You say that I am in control, not you. I want that system initialized now. I don't care if you have to kill some other system to do it. Override your protocol and start it, or are you lying about me being in control?" He stood eye to eye with her, willing her to comply. They stood there, eyes locked for what seemed like forever then he felt a change. She lowered her head.

"Very well. The system is initializing. The protocol has been altered." He nodded and started for the door, forcing his knees to lock when they threatened to dump him on the floor. After the first few steps he got into his stride and was soon running toward the stairs that would take him down to the lower levels. He focused on the newly initiating system in his mind as he ran, and could feel the power coming up in it, and the connection to the AI being made. It started to announce its presence as had the others but he ruthlessly overrode it and gave it the task he wanted completed. The systems queried his purpose and suggested a variation. He agreed and it engaged. He felt the power surge into the system, feeling the drain from others.

He turned his mind to the proximity sensors, plunging into the data they supplied like diving into a pool of water. He had to stop running as suddenly he was back in the waters around the city, plunging down, down, down, until his mind felt the jumper, still sinking slowly toward the abyss below. He sent the position back to the new system, and watched as what he perceived as an arm of light swept down from above and grabbed onto the jumper, grasping it with a pseudo hand and stopping its slow descent. There was another wrench of power that made Sheppard's stomach turn, and he slammed back into the corridor where he had stopped, his perception thrown out of the sensors as he felt the system falter and stop. He dropped to his knees again, and could not stop the urge to rid himself of his meal for the day. After that was gone he suffered through the dry heaves for several minutes before he was able to sink back against the wall and simply breathe.

He raised a shaking hand to wipe at his mouth, and was shocked to see it stained with blood. He didn't feel any pain, and upon examination could find no cut where the blood could have come from. He vaguely remembered swiping at his face earlier, at a warm wetness, and he brought his hand up to his nose, and felt the dried blood underneath it and on his chin. Evidently his foray into the database had not been without consequences either to Atlantis or him. He pushed himself up and staggered down the corridor toward the next set of stairs. He had a long way to go, and he had to keep moving. He reached out for the system he had initiated, feeling it working. He kept it in the forefront of his mind as he headed into the depths of the city.

Chapter 14-

He had no idea how long he had been unconscious before he suddenly realized he was staring very closely at the back of the base of the pilot's seat in the jumper. The jumper's lights were out, but there was some kind of glow, increasing even as he became aware of it, that was coming from outside the craft. He pushed himself into a sitting position, cursing as he felt numerous pains and aches that were no doubt from serious injuries that would soon rob the universe of one of its greatest minds, if not the greatest. Despite the horrid pain he pulled himself up using the arm of the seat and stood swaying, looking out the view screen. He blinked at what he saw. The jumper appeared to be enveloped in a ball of energy, and the ball was moving.

He could tell that because the ball seemed to have a 'chain' of like energy that disappeared up into the darkness. As he watched the 'chain' seemed to flex and draw in on itself, pulling the ball, and the jumper upward. It was very odd. However, given the alternative, McKay was not prepared to be picky. He'd take odd over sunken any day. Been there done that, fantasized about Carter in the wet t-shirt. He turned his attention to the jumper's systems. It did not take him long to determine that there was nothing he was going to be able to do here and now. It would take a complete overhaul, probably a month's full time work to get it back to working order. It appeared he was stuck with whatever had him.

He was pretty sure that a drone had hit the jumper. He was also pretty sure that Sheppard had been trying to warn him off and had been trying to save him from attack. The question was who, or what, had attacked him and why? There was only one answer that made any sense. Atlantis itself had launched the attack. If Sheppard had indeed joined to the city, it seemed the city was not prepared to give him up without a fight. It had made a preemptive strike. The question now was what was next? If the city had seen him as a threat, then the Daedalus was a sure target. Would the city try to shoot it down when they came into orbit? And what about all the people on the Alpha site? Would the city even let them come back now that it knew that the government suspected John's enhanced interaction? Would it block the gate completely, or allow them the illusion of an open gateway and then close its shield to destroy those it could. Just how far was the AI willing to go to protect its golden boy?

There was also the question now of just how much control it had over Sheppard. He certainly had not appeared to be happy with what the city had done, but it could have been an act. Could have, but McKay didn't think it had been. Sheppard had been angry, and he had tried to help, even if he couldn't stop it. Of course the implication was that Sheppard had simply become a puppet of the city, and could not be trusted, but he wasn't ready to got there either. In any event, someone had stopped the jumper from sinking to the ocean floor. He was going to take that as a good sign.

He was pulled from further contemplation of the question by the appearance of lights above him. It was Atlantis. Evidently the reboot had progressed to the point that the exterior lights were on, though he didn't recall seeing them before. Of course he had recalled any instance of a tractor beam either, and he was pretty sure that was exactly what he was currently enveloped in. Fascinating! He could not wait to get his hands on the specs for this system. Of course there was the remote possibility that Atlantis might not be letting any of them see anything anymore, but he preferred to ignore that possibility.

In a matter of minutes the Jumper was being pulled inside the city, into what appeared to be not one of the underwater hangers, but was instead appeared to be a large flooded tank. The beam disengaged and the jumper settled gently to the bottom of the tank. McKay stood there, gripping the back of the pilots seat waiting for the next development, but nothing happened. Looking out the front he could see the surface of the water about twenty or thirty feet overhead. Not particularly helpful. He supposed he could open the hatch, flood the jumper, and swim to the surface. But he was pretty sure that the water was ice cold, and he could see no evidence that there was anywhere to swim to once he got out. He could only tread water for so long under optimum conditions, and freezing water was not optimum.

He sat down in the pilot's seat, and tried the systems again. Nothing, big surprise. He tried his radio but got no response. That made sense, he was inside Atlantis' shields now, he couldn't reach the mainland and the jumper's communications were down too. Of course Sheppard should be able to hear him now, but somehow he doubted that the colonel was wearing his radio after all this time. He seemed to have very few options. He could stay in the jumper and die of hypoxia as the air ran out in approximately two hours, if he stayed calm. Alternately, he might be able to get the CO2 scrubbers working, and he could sit here and slowly starve to death as he waited for the city to rise and someone to come looking for him. In yet another exciting choice he could try to swim out and hope he could stay alive long enough to get to some ledge or something that might be on the other side of the room/tank he appeared to be in. Or, he could just end it all by shooting himself. Oh wait…he had left his pistol back at the camp, so much for the suicide thing. This was all so not fair. His choices sucked.

He was considering how many times he would have to bash his head against the bulkhead before he knocked himself out when he noticed that the water level seemed to be dropping. The jumper shuddered as the water began to swirl in a pattern reminiscent of a giant whirlpool. He was begging to wonder if Atlantis had decided to flush him back out into the abyss, when the water was abruptly all gone, leaving he jumper sitting on what he could now see was a vast white tanklike room with a domed ceiling. He wasn't sure what he should do now.

He looked out the windows, trying to see if there was any door to be seen in the smooth sides of the tank, but could see nothing. He would have to open the back hatch to see if there was something there. He pushed out of the pilots seat ad went toward the back of the jumper. He started to reach for the activation switch for the ramp then paused. What if it was a trick to get him to open the hatch, then the room would suddenly be flooded again, drowning him. Of course if Atlantis had wanted him dead he would be on the sea floor right now. He pushed the release.

He walked down the ramp, and stood looking at the huge expanse of the tank. He was located at one end of what appeared to be a room of at least 200 meters long by 20 meters wide. It was very impressive, and seemed to have no doors or access points at all, so not helpful. He trudged around the jumper, looking all around, examining walls, and shivering in the cold, damp air. After one circuit he went back into the jumper and got one of the parkas that was stored in the locker. It didn't fit great, but it was warm. He went back out, and almost had a heart attack when a voice spoke from behind him.

"I hope you brought pizza. The cupboard's a little bare."

He spun, almost falling over as he did so, and came face to face with a scarecrow figure in the latest in arctic wear. The familiar dark brown hair was like a wild bush, the beard was matted with blood, the skin was pale, and the dark eyes were glazed. Before he could recover from his shock enough to let loose with some sarcastic remark regarding a brain and a little girl from Kansas, he had to lunge forward to keep Sheppard from doing a face plant on the wet floor. He sank to the floor under the weight, even as he noted that it didn't seem like it was enough. What did he do now?

He slowly turned the limp figure he was holding until he was looking down in to the unconscious man's face. He grimaced at the blood, which he could now see must have been from a nosebleed, and a recent one at that. He felt for a pulse on the neck, and felt a steady throb that seemed to be okay. But from the feel of the skin, sweaty and clammy, he suspected that the man was in shock. All of Beckett's training came cascading back through his mind. He needed to elevate his feet and keep him warm, not easy to do in the bottom of a giant tank with a dead jumper in the middle of a sleeping city. He looked frantically around trying to generate an idea. However while physics he could handle with his brain tied behind his back, this was not something he was good at. He decided on trying something else. He patted at Sheppard's face.

"Enough with the drama, Colonel. I've had a hard day, and I don't have time for your theatrics." He patted a little harder, and was rewarded by a faint moan. A few more pats and the hazel eyes were fluttering open, and staring at him in confusion.

"It was all a dream then?" Sheppard mumbled, flopping a hand limply against McKay.

"Well despite the fact that you dream about me, which is incredibly disturbing on many, many levels, Yes, I am real. And I would like to repeat my last question, which was, if you recall before all the shooting and the sinking, 'What the fuck?' I repeat it now with emphasis." For a long moment Sheppard only lay there and blinked up at him, and McKay was beginning to think that maybe Sheppard hadn't been talking to the AI, maybe he really was nuts. But just as he was trying to think of a way he could somehow restrain the man, the hazel eyes blinked at him again and where the ones with which he was so familiar.

"I'm sorry Rodney." Sheppard said, pushing himself up and away. He ran a hand through his bushy hair and scowled down at the floor. "I couldn't stop her in time. She thought you were going to try to take me away."

"She?" McKay asked. Okay, still edging toward the nutty here, but he sounded lucid enough. He scrambled to his feet as Sheppard levered himself up, swaying a little, though he waved of McKay's offered hand. He closed his eyes for several moments and seemed to steady. He let out a breath and opened his eyes, looking around the tank.

"Not the best place for explanations. Let's get what supplies we can out of the jumper and go back to the control room. I have a place set up. It's small and kind of cold, and not exactly fragrant at this point, but hell, its home. There are no transporters so we'll have to walk. If you're a good boy I'll tell you a story as we walk home."

"Goody, a story." McKay snarked as he followed Sheppard back toward the jumper. He hated hiking, and they were at least half an hour and four levels below the control room. He was just glad they weren't off on one of the piers. Well at least the story should be interesting.

Chapter 15

"…and that's when you showed up and told me how the SGC was going to haul me back to earth for use as guinea pig and take me away from her. She's gotten kind of attached, in a Glenn Close kinda way, and kinda made a preemptive strike."

"So you and the AI are linked, and when you read the message she could read it too?" Sheppard could see that McKay was getting all of this, cataloging it and he could almost see the questions that were hovering in the background waiting to be asked.

"Yeah. I can stop it if I try, but I wasn't expecting something like that, and I didn't turn it off. I tried to convince her, them, that it would be okay, that you wouldn't turn me in, but she didn't believe me. I wasn't quick enough to warn you off. I'm sorry, Rodney. You know I wouldn't hurt you." Sheppard hoped that McKay could see the sincerity in his eyes, and knew that he was telling the truth. They were almost back to the control room, and Sheppard had given him a synopsis of what had happened to him over the last two months. Sheppard could tell that McKay's mind was reeling at the thought of the information they could access through Sheppard's link to the city, but he knew was glad he was suppressing those impulses. If he acted like a scientist with a new lab rat, he had a feeling that McKay's next month was going to be very uncomfortable. The same idea must have occurred to the scientist as he cast a look at Sheppard.

"How did you convince her to help me, and what exactly was that? It appeared to be some sort of tractor beam," he noted. He was not able to keep his enthusiasm hidden when he said the words 'tractor beam' and Sheppard broke into a grin.

"Cool it, Scotty. That wasn't a tractor beam; it was a specimen collection arm. Short range and very limited uses only. I had to do some fast…'talking' to get the Atlantis to use it like we did." Sheppard said with a snort. McKay frowned at him, obviously expecting more info. Sheppard resettled the pack he was carrying on his back, more tired and achy than he wanted to admit. He was glad he was able to move at McKay's speed. Forcing the interface had taken a lot out of him. He felt like he needed a nap. McKay, impatient as always, reached out and grabbed his arm.

"Details Sheppard, I want details." He demanded. Sheppard pulled his hand off, and looked around for the avatar. So far she had left them alone, but he suspected, no knew, that they were being watched, and he didn't want the city misinterpreting anything McKay might do. He was blocking his thoughts from the joining, but that didn't mean the city wasn't listening to every word along with watching.

"Keep your hands to yourself McKay. We don't want any boiling Canadian bunnies now do we?" He asked with what he hoped was a suitable warning look. McKay looked down at his hand, startled as if he hadn't even realized it had clamped on Sheppard's arm, and pulled hastily away. He looked around in a manner that Sheppard was sure that McKay thought was subtle, then looked back at the colonel.

"Maybe you could share a few further details at your leisure then. No hurry, really. We have another month. Not like we need to have everything out right here and right now. Otherwise what will we have to talk about? Perfectly willing to wait until you're ready. You let me know." He walked casually on, all the while studying the walls as if he expected ninjas to jump out and attack him at any moment. Sheppard shook his head and chuckled.

"Just a little thick there Rodney. I don't have any waders. Could we keep the BS to a minimum? It's an AI that's older than our species, I have a feeling that she can probably read you from about a mile away." Not that McKay had ever been able to fool anyone. But that had been pathetic. The scientist threw up his hands.

"Fine. I am tired of walking on eggshells here. Is it going to kill me or not? If it is could it do it now before we tackle the last of the unending stairs? I'm getting a cramp, and death may be preferable at this point." He shrugged the pack he was wearing around trying for a more comfortable position. Sheppard couldn't hide the grin that split his face. He had really missed McKay's histrionics. The scientist scowled at him. "Oh sure, fine for you. You're the golden boy, can't do no wrong. Put yourself in my place. See how you like being the messenger of bad news. Try to help a friend out and get shot for your trouble why don't you." He practically bellowed the last at the walls. He glanced at Sheppard. "Is it even listening?"

"Probably," He said with a shrug. "She's kinda not talking to me right now. I think I may have pissed her off a little when I got a little bossy about saving your ass. I made her start a program out of sequence." McKay stopped in mid step, his foot hanging suspended over the next step. He then almost fell over as he tried to turn to Sheppard and take the step at the same time.

"What!" He yelled, grabbing Sheppard by the shoulders and shaking. So much for the watching the hands thing. "You forced it to alter its protocol? How? What did you do?" There was no backing off in McKay now. This was all scientist, all Rodney. Sheppard shook his head and pushed past McKay and kept going up the stairs.

"We're almost there. Let's get sat down and maybe have a cup of tea, or some of that instant coffee from the jumper. Even that stuff will taste good at this point." He said. He really was tired. Getting more so all the time. He just wanted to sit down and have something warm, and maybe wrap himself in one of Teyla's blankets. He suddenly realized that for the first time in almost two months there was no other presence in his mind. He missed it more than he thought possible. He felt like that little boy again, the one that had watch a pine box with his mother in it being lowered into the cold ground. That feeling had started to go away. He found himself blinking away moisture from his eyes, and bit his lip to keep from calling out to the avatar. The city had been wrong; he couldn't let it go, even if it cost him the thing he hadn't even realized he wanted so much.

They climbed the last of the way in mostly silence, except for the usual complaints from McKay. It was strangely soothing to have McKay griping in his ears, even as he dealt with the loss of another familiar thing. He led the way to the conference room, and lowered his pack next to his small cooking area. He waved an arm expansively to McKay who was standing in the doorway staring, plastering a fake smile on his face as he spoke.

"Home sweet Home, Rodney. Pull up a chair and make yourself comfortable. Unless you crave solitude this is where we'll be living for the next month. Take it from me solitude isn't all it's cracked up to be." Taking McKay's unusual silence for consent he went about putting some water on to boil, and scrounged through his meager supplies looking for the last of his tea. It was a celebration after all. And anyway, there was coffee in the supplies from the jumper. They could have that for a while when the tea was gone. He ignored it as the other man walked around the room, looking at his nest and the boxes of emergency cookies. He was focusing on the tea so hard that he was almost shocked when the soft question came.

"Is this all you've had?" Rodney was standing by the emergency cookie cases, but was looking at Sheppard. He shrugged.

"Well I had some MREs and there was some stuff in the quarters." He didn't feel the need to say just exactly when those had run out, but he had a feeling that McKay suspected anyway. Maybe he had lost more weight than he thought. He thought that maybe McKay was afraid it was all they had to eat now, so he tried to put the best spin on it he could. "There's food for four for a week in the jumper. So we can stretch it at least two weeks for the two of us. That's not counting any food stashes that you may have had that I didn't find. Probably live high on the hog with that for a month, huh?" His false cheer fell flat. Rodney was studying him like he was one of the ancient devices, which he guessed he basically was now. Without warning the scientist stepped over until he was standing in front of Sheppard and he reached out and pulled the zipper down on the parka, and pushed it off his shoulders. He then pulled up the layered shirts and looked at the exposed abdomen and ribs.

Sheppard winced as the cold air bit into his skin, and he was about to protest when he looked down at himself. His ribs were showing through so much that you could count them easily through the skin, and his stomach was pulled back until it was concave. His pants were drooping so much that his hipbones, much more prominent than they should be were also poking out. He was faintly startled. He hadn't really been paying attention, really. It simply was what it was, and there wasn't anything he could do about it, but now he looked at himself through Rodney's eyes. His horrified eyes. Not good. Before he could speak McKay dropped the shirt and pulled the parka back around him, even going so far as to zip it back up. When he was covered again he found himself speared by the blue eyes.

"You look like an ad for Anorexia. You didn't think to mention this when we talked?" he said quietly, which meant that he was really, really upset. McKay was never quiet. Sheppard turned back to the stove and checked the water.

"There wasn't anything anyone could do, Rodney. Why talk about it? Carson would have gotten all upset and for what?"

"For what!" Okay, so much for the quiet. "You were friggin starving to death and you didn't think that was something we needed to know? Didn't you think we might notice when we came back that your skeleton was cluttering up the conference room?"

"I wasn't going to die, Rodney. I have enough emergency cookies to make it through, or I did before you got here. They give you 2300 calories per cookie. Now we have the MREs from the jumper and maybe by the time we run out of those we can start doing some fishing down below. The lower levels where the fish are will be opening back up in five or so days." He frowned. "Well they were supposed to. I don't know what might have changed." He decided not to dwell on just what Atlantis might do. "The biology guys reported to you, you must know what's edible and what's not, right?" McKay ignored his distraction gambit with a wave of his hand.

"Not going to die? 2300 calories per cookie? It's 5 freaking degrees Celsius in here, if that. You are probably using 2300 calories a day just being alive in this. And that doesn't count any activity. I know you were making a daily pilgrimage out to the balcony, what else were you doing?" Sheppard looked away.

"You were exercising weren't you?" When Sheppard merely looked back at him McKay flung his hands up. "I do not believe you!" He ranted. "What, are you trying out for the roll of the best looking starvation victim? I can hear it now…"Well yes he's dead, but look at the muscle tone on his body. Wish I could do that'. You'll be the envy of Hollywood stars. They'll name a diet plan after you, just like that one they named after the health nut doctor who died while exercising. Your estate will make tons of money. Books about the John Sheppard diet will fill the bookstore shelves. Soon everyone will be fashionably emaciated. Yes, good times ahead." He threw himself into the chair and sat there scowling at Sheppard who stood before him gnawing on his lower lip in silence.

They stared at each other for several minutes before Sheppard turned and checked the water. It was just under boiling. He took it off the heat and set it aside, dumping some tea in to steep. He could practically feel McKay's eyes on his back. He sighed.

"There wasn't anything you could do, Rodney." He repeated in a low voice, addressing it to the tea. He really hadn't wanted to think about just how hungry he had been, or if he were going to survive until the city rose. He hadn't wanted to burden his friends with the knowledge either. He knew how he felt when there was nothing he could do, and he hadn't wanted them to feel that same way. There was a snort from the chair that sounded suspiciously like it was hiding another sound, but he didn't turn. He would give McKay his dignity. He owed him that at the least. After a few sniffs that could have been from the cold, Rodney cleared his throat and spoke.

"Yes, well be that as it may, we have some food now, and you can use some of those God awful things as a snack to fill in between MREs. I may have listened to a few of the reports from those fish fondlers who call themselves biologists. They did a few fish fries and came up with three or four species that were pretty fair eating. I think a few were caught in the lower levels. We should be able to find something though you'll have to catch it, and clean it, and cook it, as I not Dan'l Boone or Euel Gibbons." Evidently the subject of his eating habits was going to be forgiven. He was grateful for that, and turned to look at his friend.

"Yeah, I never really thought of you as an outdoorsy kinda guy, McKay." He joked, moving to stand in front of the chair. "More of a call for pizza type."

"Yes well genius doesn't pause lunch breaks. If all our ancestors had been too busy hunting down their next meal to think about a more efficient way to get that meal, we'd still be beating small rodents with a club and eating whatever grubs we could find under a rock."

"Guess we owe Oog McKay a debt of gratitude for coming up with that sharpened stick thing. Best thing since that one ape picked up the thighbone and hit his his buddy with it. I can practically hear the theme from 2001 as we speak." Sheppard tried a smile, and was glad to see the humor spark in McKay's eyes. God how he had missed this. Food he had not missed, much, but this simply being with someone else. Having someone to talk to, to snark at. That was what made his life full, what gave it meaning and depth. As much as Atlantis offered him, it was nothing compared with this.

McKay started to reply when the Avatar suddenly appeared right behind the chair. The scientist noticed the shift in Sheppard's attention and stood to look. It was obvious however that he could see nothing as he turned back to Sheppard who was watching the avatar warily, ready to move it she made a move on Rodney. She hadn't been able to touch him, but he couldn't take that chance.

"What? What are you looking at?" McKay demanded. "You were doing this on the balcony, like you were talking to thin air. Don't tell me you've actually cracked. I do not want to spend the next month doing the Atlantis version of the shining. You are no Jack Nicholson." Sheppard pulled his attention away from the avatar to grin maniacally at Rodney.

"Heeer's Johnny!" He intoned, smiling at McKay's snort of derision. The Avatar was watching them, looking from one to the other as if studying their interaction. Sheppard was aware that there was a good possibility that the AI was reading his emotions. He couldn't block those as easily as he could his thoughts, not when he felt such relief at finally having someone else to talk to, to see, to simply be with. He also wondered if the city could read Rodney to a degree. He was after all a gene carrier now, and that had to give the AI some access. Maybe it was time for some more questions. He waved a hand at the avatar.

"I guess you can't see her, but the city has an avatar, a physical representation of the AI. She says that the ancients found that it was more psychologically satisfying for a newly joined person to see someone when they talked to the city. Made it more real I guess." He explained. McKay spun on his heel and peered at the area Sheppard had indicated, as if by merely trying he could see what Sheppard did.

"She?" He asked snidely. "Why am I not surprised at that 'Captain Smirk'. Why can't I see her? I have the gene too."

"This representation has significance only to you, John. If Dr McKay were joined, he would see us as someone of equal significance to him. However the nature of his genetic tie to this system precludes such a joining, as we had discussed before." The avatar answered the question even though it had not been aimed at the AI. Obviously the city was prepared to deal with this on some level without hostility. He smirked a little at the answer, causing McKay to ask again.


"Looks like you can't fool Mother Nature, Rodney. Your mouse gene just doesn't hack it. No joining for those with counterfeit genes. Sorry." It felt good to play 'taunt the geek'. It had been months since he had indulged in his favorite pastime. McKay sputtered, his chin rising pugnaciously.

"So this club is exclusive to 'natural' gene carriers only." He sneered, making the word sound like something dirty. "Are there separate water fountains we lesser mortals should be using, or perhaps we can start sitting in the back of the puddle jumpers?" He suggested. Sheppard had a feeling that Martin Luther King had nothing on Rodney McKay when it came to integration issues. Rodney had a dream. He saw the avatar was studying McKay closely. He loosened his control a little, and felt a surge of the awareness that he had missed as the AI delved into his mind for meaning. The avatar raised an eyebrow.

"He is accusing us of discrimination." She said in surprise. Sheppard smiled and nodded. The avatar looked at McKay again with a thoughtful look on her face. Evidently the AI was considering something. Finally she looked back at Sheppard. "Interesting. This gene therapy was based on your genetic structure. In a way he is a child of Neelam as well, a sort of adopted son, as are the others that had the therapy. Those who came before considered a child of adoption the same as one of blood. We must consider this." She disappeared.

"Good going McKay, you scared her off." He turned with a smile and poured some of the tea into a cup and the rest he poured slowly into one of the small empty water bottles he had kept. He handed the cup to Rodney who was studying him with narrowed eyes.

"What did she, they, it, say about me?" he blurted. Sheppard causally took a drink.

'It's not always all about you, Rodney. Sometimes it's about other important things." He teased. McKay waved the thought aside as if there were no more important things.

"The city tried to kill me, and now I'm here having tea with its golden boy. Consistency, colonel may be the hobgoblin of little minds, but it is also the touchstone of ancient technology. They were a little anal when it came to computer practices."

"Really? I hadn't noticed that particular issue in scientists before." Sheppard said and settled on the edge of his nest. He was still really, really tired. He set the bottle down and let himself fall over to the side, nestling down into the pillows. Maybe while the city contemplated the end of Apartheid he could catch a little nap. He was sure that McKay could keep himself busy. He drifted off on the thought that at least there would be someone there when he woke up.

Chapter 16-

Rodney looked up from his tea, tea without any sugar in it he might add, ready to put Sheppard in his place, and noticed that the colonel had fallen over to his side onto the pillows of his bed and now seemed to be deeply asleep in the moments since he had last spoken. He gave a soft snort, and finished his tea, grateful for the warmth even if it was bitter. He cast another look around the room.

He once again felt the twist in his stomach as his eyes fell on the two cases of emergency ration cookies that sat near the small camp stove. He shifted his eyes back to the sleeping colonel, and felt the twist grow even worse. The man was a walking skeleton. You could cut yourself on his ribs, talk about a lean and hungry look. Up close even the hair looked thinner, it was probably ready to jump ship and search out a new victim to parasitize, there couldn't be much nourishment available from Sheppard's scrawny carcass.

He looked from the sleeping Sheppard to the pile of blankets and tables he had formed as a sort of nest, knowing the reasoning behind it, but still feeling bad because his friend had been forced to live like this for two months alone. He was angry that Sheppard had kept all this from them, though he did understand why. They could have done nothing about it, and the knowing would have been worse than the not knowing. But still.

He put the cup down quietly and stood from the lone chair that made up all the furniture in the room. It looked as if he was on his own for making arrangements for accommodations. A look at Sheppard's little fort showed him that if they turned the mattress sideways they could fit another of them in there. That way they could share body heat and the blankets. It was a little bit more togetherness than McKay was strictly comfortable with, but he was not going to complain about being warm. He was also strangely reluctant to leave Sheppard alone for any amount of time, now that he was there.

He trudged top the nearest quarters, and what a hike that was without any transporters than you very much, and found it had already been stripped of its mattress. Okay, on to the next. It wasn't his own orthopedic version, but it would have to do. He dragged it back to the control room, leaving it there so that he didn't wake Sheppard. He then went back down to his own quarters, and who exactly had decided that he needed to be such a schlep from the gate room? Sheppard's and Weir's were a level up and closer in, what was up with that?

He carefully removed the hidden panel under his desk and started pulling the MREs that were hidden there out. He stopped when he realized that there were only half as many as he expected. Where the hell? He felt around inside the wall, and found a piece of paper. Pulling it out he was not too deeply surprised to find Ronon's cramped printing offering an IOU. Damn it the man found every hiding place he had. He must have the nose of a beagle, and damn if he hadn't eaten all the meatloaf.

He packed the MRE into a duffle bag and checked the rest of his stashes. Evidently Sheppard had found all of those. His candy was gone, as was his soup stash. Talk about mixed feelings. He was slightly narked that the man had raided his room so effectively, but he was more upset that he had hidden the MRE so well. Sheppard could have used them. He felt as if he had taken the food out of the man's mouth. Shaking off the mood he started digging through his dresser looking for his cold weather gear. He was soon outfitted in long underwear, two shirts and a pair of snow pants. He replaced the too big parka with his own, and found some gloves that made his hands feel much better. He gathered the rest of what he thought he might need and took it all back to the control room.

A quick glance inside showed that Sheppard was still sleeping, though he had pulled one of the blankets up and over his head sometime since McKay had last been there. Rodney put the duffle bag down near the other food, if you could dignify the stuff with the name, and wondered back out to the control room. He wasn't sure what he could do with himself at this point, as nothing was working, at least anything that did him any good. He could take the long walk down to his lab, and find some of the uncataloged ancient devices, but given their track record with the things, it might not be wise to try them out without a fully staffed infirmary available.

He rolled one of the chairs from the conference room that Sheppard had moved out over in front of the door to the smaller room and sat down so that he could see Sheppard should he stir. By turning the chair he could look out over the gate room. He swiveled around and stared at the star gate as he pondered what had happened.

Sheppard was 'joined' to the city. That confirmed that theory, and evidently the city wanted to keep it that way. That the city was more than capable of 'protecting' Sheppard was a given. McKay was sure that there were weapons here that they still had no idea even existed. As it was the drones were enough to make sure that anything that they had was not going to come barging in here and take Sheppard by force. The only fly in Atlantis' ointment was the fact that what she was protecting was not as invulnerable as she, or as unconcerned with physical needs. She might be prepared to withstand another siege, after all she had withstood the wraith, but Sheppard was already on the edge of starvation. Another few weeks and he would be dead.

Of course the star gate would be available then, and Sheppard could conceivably go forth and gather food, but then the city would have no guarantee that he would return, and given the dangers of Pegasus in general, there could be no guarantee, even if Sheppard were willing to make such promises. There were too many enemies out there who would love to get their hands on Sheppard just because of who he was. They didn't need the extra incentive of his new connection.

McKay pondered that issue. What was he going to do about Sheppard's new little friendship? Talk about friends with benefits. His best friend was suddenly a repository of ancient knowledge, or at least was able to access such knowledge with a thought. The very thought made his head spin. He knew what the people at the SGC, at the IOA, would want, what his scientist side said he should want. He had to decide where his loyalties lay. He swiveled slightly to look at the sleeping man.

In his sleep the colonel's slimmer than usual face was peaceful, and even with the beard incredibly young. If McKay turned him in that peace would be gone, and his youth, that bubbling pool of defiant life that so defined John Sheppard, would be sucked out of him in a manner that no wraith had managed. McKay could not do that, could not allow it to be done. No matter what the cost to science, to himself personally in terms of his own theories, he would not sacrifice this one man to it. A huge burden seemed to lift from his heart, one that he had not recognized as having been there since the call had come from the Daedalus.

As he reached his conclusion he turned back to the gate room, and found himself staring instead at a woman standing before him. She was dressed in the manner of the various ancients they had encountered, in flowing white robes. She was tall and thin, with hazel/green eyes that were strikingly familiar as was her face in general. What really sparked his recognition was the hair though. It was short, only chin length at its longest, but the top was a spiky mess. The whole picture together was inescapably Sheppard in female form. The image smiled at him.

He leapt to his feet and retreated back so that he stood in the doorway of the conference room. He wasn't sure if he was trying to protect Sheppard or if he was simply making it easier to run to Sheppard for protection. In either case it caused the smile to grow on the familiar face.

"You need not fear us Rodney McKay. We will seek to harm you no further." She said.

He cast a look over his shoulder at the still sleeping Sheppard. Did the man have no instincts left at all? There were things going on here, how could he sleep? He looked nervously back at the woman, no, not a woman, the avatar. This was the representation of the city that Sheppard had spoken of. He could have mentioned the fact that she looked like his mother, or what McKay assumed was his mother. Had to be. The question was why was he seeing her. He had thought that was only for Sheppard.

"We have decided that as you carry the same gene as John that we will continue to treat you, and those who also have had the therapy, as a citizen of this city, as we have done previously. No joining will be possible for you, but you will not be excluded."

"Oh…oh well…that's very good." He stuttered. He hadn't been aware that not being allowed to even interface with the city as he had before had even been in question. What else had Sheppard not thought important to share? "And the other natural gene carriers?"

"They will be allowed access as before of course. They would be allowed joining, though only a very few have sufficient levels to allow full compatibility as John does. It is of course improbable that such an opportunity will arise given the circumstances surrounding this occasion."

"Yeah…about that. Is there any way that the program can be locked so that it can only be accessed by a very limited number of people?"

"John may flag the program as protected. Only those he wishes to have access would be allowed."

"Just how much access does Sheppard have? As compared to everyone else?" he clarified. He needed to know. The more there was to protect the harder it would be, the less people could know.

"Normally those who live in the city are given general access to approximately 60 of the systems. Most of the 'natural' gene carriers as you call them have received this level of access in the past, and will continue to do so. Those with the gene therapy have been allowed a slightly lower level of access as there was some confusion regarding their status. That confusion has been resolved. You have given yourself access to the more sensitive systems that are normally not available to the general public, due to your intrusions into the system using your technology. As we had no orders to the contrary this intrusion was allowed. You have access to a total of 88.689 percent of the available systems in this way."

"And Sheppard?" He had a feeling he already knew that answer, but he wanted to hear it from her, them, it. He really had to decide on a pronoun and stick with it.

"He is now allowed free access to 99.879 percent of all systems, excluding only those systems which are concerned with my own program. He would be allowed access to the remaining systems should maintenance be required." In other words, Sheppard could access anything except the AI itself, and even that had a back door.

"And other facilities?"

"All other facilities created by the builders would recognize his genome. Those not containing a program similar to our own would allow full access." That grabbed McKay attention.

"There are other facilities out there with AIs?"

"Yes." She, they, it…. damn it, the AI, didn't elaborate and McKay didn't push it. There had to be a list somewhere, and if Sheppard had access…He turned his attention to more important matters, like how this affected him. "If Sheppard ordered you to allow us access to all your data files would that be allowed?"

"If he so ordered. As stated he is allowed full access. It is his to designate. You would of course have to use the view screens for such access."

"Well that goes without saying…Doesn't it?" What was she saying? Something else Sheppard hadn't mentioned? They were going to have a very long talk when the colonel woke up.

"John can access such data via direct neural interface. He can choose to simply view it or he may download the information for long term storage in his memory."

"He can download information directly into his brain? In a controlled manner? Anything, anything at all?" It was like the archive devices, but without the weird head grabbing action. He could almost feel himself turning green at the thought.

"Envy is the deadliest of the sins, McKay." Came a drawling voice from behind him. "The next thing you know you'll be obsessing that my…brain is bigger than yours." Rodney jumped, having not noticed that Sheppard had woken and had come to lean in the doorway. The man was smirking at him.

"As if anything you have is bigger than anything I have." McKay sneered at him. Sheppard's self-satisfied smirk did not diminish. Time to counter attack. He waved at the avatar. "Mommy issues much?" He knew that he had scored when Sheppard's eyes shifted away and the smirk faded.

"Like I said, they pick a familiar figure, so that the person joining is more…comfortable with the interface." Sheppard said with a definite defensive air. Rodney was about to make a comment when the avatar helpfully joined the conversation.

"And since those joining are usually in their infancy the mother image has been determined to provide the most efficient interface." McKay could feel the smile growing on his face as he listened to the explanation. Sheppard buried his face in his hands.

"You didn't have to mention that did you?" He mumbled to the avatar. She smiled at him.

"Oh no, no, no. She definitely should have mentioned that." McKay begged to differ. His mind was flying through the possibilities. Of course the city would have interfaced with those born inside her as soon as the child started to form its own personality, say around two. What better way to assure that the child was a willing participant than to give the avatar a familiar appearance? He grinned at Sheppard who was studiously not looking his way. "So at this point you're the mental equivalent of a toddler?" Sheppard's eyes snapped to him and narrowed.

"You may want to remember who it is that can tell the city not to listen to a certain scientist, McKay. Be a shame if certain people could no longer open the door to their quarters or pull up a system on their laptop." He threatened.

"Now, now. Mustn't be greedy with our new toys. Sharing is one of the first lessons you get in preschool. Wouldn't want the other kiddies to think you're slow would we?"

"McKaaay…" Yes, things were getting back to where they were supposed to be.

Chapter 17-

Elizabeth sighed in satisfaction as the jumper settled into the deck of the hanger bay. She was instantly on her feet and waiting at the rear door, joined by Teyla, Ronon, and Beckett. Caldwell, sent along as the representative of the SGC who had some serious questions that had not been answered so far, hovered in the rear of the group. She hit the release, and the ramp started to drop. As it reached halfway, the two people that she had longed to see were standing there waiting. She could feel a burst of cold air as the ramp continued to drop. Evidently the city's heaters had not yet managed to counteract the deep cold of its forced hibernation.

Rodney was almost startlingly hairy with a full beard of reddish brown. It seemed that a month had been more than enough for him to fill it in. His hair hadn't grown much, but it was longer. He was still dressed in insulated pants and an unzipped parka. She could tell he was wearing several layers of clothes beneath it, as he appeared rather lumpy. He was smiling however, and she took that to be a good sign. She turned her attention to the other man.

John was definitely even thinner than he had been before. Where previously he had been exceedingly fit, he was now simply frightfully thin. His face was covered by a full beard, somewhat better trimmed than McKay's, and his dark hair was a shaggy mess, well beyond anything the military would allow even at its most lenient Pegasus Galaxy mode. He too was wearing insulated pants, but had evidently shed his parka and stood there in only a long-sleeved shirt, though she could see he was wearing layers as well. They did nothing to hide the fact that he was painfully thin. His wrists, exposed by the sleeves looked like knobs. She had to bite her lip to keep herself from crying out at the injustice of it. The man had not deserved this, and he did not deserve what was to come either, but she had no recourse. But that was later, and for now she could follow her own desires, and those had her stepping forward to wrap the thin figure in arms that were too aware of the fragility that was so at odds with what she knew of John Sheppard. He returned the hug with the usual awkwardness, but with a huge grin.

"Welcome home!" he said cheerfully, as if she had simply been gone for a few days on vacation. His smile encompassed everyone, though it might have dimmed slightly when he encountered Caldwell's gaze. Typically McKay quickly filled in the silence.

"Yes, yes, we're all happy to be back and now that everything is finally functioning again maybe we can skip the hearty 'hail fellow well met' moment and get to checking systems." He threw a look over their shoulders. "Zalenka didn't come with you? Is he slacking on the Daedalus? He and Hermiod doing each other's hair or nails or something?" He raised and eyebrow in inquisition while hugging Teyla who had done the same to John previously. Ronon was simply hovering in the background, within arms reach of Sheppard and looked to be staying there, no matter what anyone said. Elizabeth smiled at McKay.

"Dr. Zalenka is on the Alpha site in titular head of things along with Major Lorne until we have verified that everything is okay for them to make a connection on the star gate."

"Well, I would have been doing just that, but since the city only rose literally moments ago, and there you were hovering like a vulture over road kill…guess what, I haven't been able to work it in. Maybe we could go now?" He started edging in the direction of the door. Sheppard rolled his eyes at his friend and jerked his head in the same direction.

"Don't mind grizzly McKay here. He's gotten used to not having to play nicely around others. He'll get his manners back once he's been socialized a little. I say we lock him in a room with Miko and Kavenaugh and let him get back up to speed all at once." He led them out of the hanger bay, following McKay's rapid retreat. "It's good to see you all. Got kinda lonely for a while. Then Rodney showed up and things got kinda crowded. It'll be nice to have a buffer again. A few hundred other people around and McKay will be a lot easier to take."

Well the sniping was certainly the same as usual. John's regular deceptively casual slouch was also the same, a fact that made Caldwell snort a little as they followed him toward the gate room. By the time they arrived McKay was seated at the main consol and was typing away on his single laptop. He was muttering under his breath as they entered. Sheppard went up and clapped a hand on his shoulder.

"We have guests dear. You can visit the porn sites later. Don't embarrass me now snookums." McKay batted at his hand and turned to scowl at him.

"Some of us have work to do now, Sheppard, unlike others who can continue their days of laziness and sloth. Maybe you can go finish that comic book you found in Kavenaugh's quarters, now that Ronon is here he can help you sound out the words. After three months won't it be nice to finish it?" Before the snark could escalate Elizabeth stepped in.

"Rodney, how long until we can get an answer on the gate?"

"Since I haven't even got it to the point where the heaters are on yet, I would say at least…I don't know a few minutes at the least. I have to verify that the system is completely rebooted and that our technology is still interfacing with it. We don't know what might have been reset. Then once I get the security protocols reset I can start verifying the power systems and-" She raised a hand and he stopped.

"Why don't we all go away and let you work?" She suggested. McKay snorted and spun back around and started typing again. Elizabeth turned to the others. "Why don't we go into the conference room and share what's happened?" She knew that Caldwell had some questions, and Beckett had been hovering about a foot away from Sheppard Since they had come out of the jumper. She had to admire his restraint. She turned toward the smaller conference room and was halfway across the floor toward it when she realized that the furniture seemed to be stacked outside the room. She stopped, confused and threw a look at Sheppard. He gave her the little scapegrace smile he usually reserved for when he had been caught at something like shooting water balloons at scientists from the balconies with an improvised catapult.

"I uh…kinda had to redecorate." She continued her path and stood in the doorway. He looked over her shoulder and gave her a shamefaced shrug.

"Welcome to Casa Sheppard. All the amenities, except for running water, and heat, and meals, but other than that what more could you ask?" Her eyes went over the improvised shelter with two mattresses and a pile of blankets, one of which she recognized from the pattern as her own. A camp stove was set up in one corner, and two conference room chairs were sitting next to a small, improvised table with a chess set on it. A game was in progress. She wasn't sure if she wanted to laugh or cry.

"Maybe we can use the other conference room upstairs." She suggested calmly. She didn't know about Caldwell, but she certainly wasn't seeing anything that indicated favored treatment or some kind of connection with the city that gave John more control than he had before. She wasn't sure if she was relieved or saddened. She knew she did not want John taken away, even if it was for the 'good of the human race'. She had almost laughed when some suit from the IOA had dropped that particular phrase into one of the near daily messages that the Daedalus had relayed from its position halfway between the Milky Way and Pegasus galaxies. She had been very grateful when it had been time for the big ship to leave its station to come and pick her up to go back to Lantea. But as much as she knew what the impact would be on Sheppard, she knew that if the hypothesis had been proven to be true, then they would have been given access to an almost endless supply of data, data that might have allowed them to defeat the Ori and secure Earth permanently. She could not discount the value of such a thing. What was one life against that, a life that she knew John Sheppard would have been willing to give on the battlefield. Whether he would be willing to give it up in the laboratory was a question she hoped she would not have to ask.

They climbed to the room that they used for mission briefings and sat. Beckett grabbed a chair next to Sheppard and rolled his chair over until he was side by side with the colonel who raised and eyebrow at him.

"Gee Carson, I missed you too, but people are going to talk." He drawled leaning subtly away from the Scots doctor. Becket was having none of it and reached out for Sheppard's wrist.

"You look like you need a few good meals, lad, and if you get cheeky with me I'll be sure that they are administered via IV with a large bore needle. Now hold still." He proceeded to take his pulse and looked into his eyes. He then snaked a stethoscope out of his pocket and started to lower the zipper on the shirt. Sheppard slapped at his hands.

"Jeesh, Carson, buy a guy dinner first why don't you?"

"Maybe you could wait to do your exam until we finish here, Carson?" Elizabeth suggested. The doctor settled back in his chair with a huff, pushing away slightly, but not so far that Sheppard could make a break for it. He meant to get his exam in. Sheppard sent her a grateful look and tugged the zipper back up. It was still quite cold in the room, and she wondered how much longer it would be before the environmental controls were back on. She saw the impatient look on Caldwell's face and thought she better get down to business before he did, and she knew that John would not take that well. He never did when something came from the superior officer.

"I'm sure that Rodney told you about the news we got from the man claiming to be Margraves." She started, looking in Sheppard's eyes. She saw anger flash there, and something else she could not identify.

"Yeah, He filled me in. The trust seems determined to get their fingers in our pie one way or another." She could detect no hidden meanings in his words or his demeanor. "The boys…" He glanced at Caldwell, "I'm sure that the interrogation was handled in an appropriate manner."

She smiled slightly. She knew that he was not sure of anything of the kind, but was hoping it had not been done where Caldwell would find out about it. She set his mind at ease. "All completely above board, colonel. Major Lorne handled it very well. Everyone was quite pleased with his results."

"Too bad the whole thing was based on a bad hypothesis." Sheppard said baldly. "Makes the whole thing almost worth it to think about the Trust finding out it was all for nothing. They went to a lot of trouble for nothing." There is was-out in the open. Typically it was Caldwell who pounced on it.

"So you are saying that despite being here during the reboot that you have no more control over the city than you did previously?" He was studying Sheppard closely. The Lt. Colonel's eyes met his squarely without blinking.

"Yes sir, that's what I am saying. I don't know where they got their information, but evidently someone somewhere misread something, or maybe I just don't have enough of the gene to do what they described. Whatever it was, nothing happened here beyond a stretch of solitary on bread and water. There are those who might say that was deserved in any event." He added with dark humor. He waved a hand out and down.

"You saw where Rodney and I were living. I can show you the MRE packets and emergency ration packets for the only food we've had. You can feel how cold it is, and this is damn near balmy compared to what it was before. If I were in control of the place you can bet it would have been a damn site more comfortable. You have my word as an officer that I am exactly the same as I was before the city sank, and so is Atlantis." The two men held each other's gaze for several seconds before Caldwell looked away toward Elizabeth.

"Dr Weir?" He asked. She nodded and looked at John with what she hoped he understood was a remorseful look.

"I'm sorry, John, but the SGC wants a battery of tests to be run on you to verify what that nothing has happened. Not," She added with a raised hand, "that I do not believe what you are saying. It is simply to make the people at the SGC and on the IOA happy. Carson will run the tests and we will send the results through on the first data burst to Earth once the stargate is working. I'm sure that once they understand that nothing has happened, and that the Trust was mistaken, that this will be the end of it."

Sheppard looked upset, but he did not protest beyond a slight pout and a greater slouch into his chair. She was about to ask him about his ordeal when a blast of warm air suddenly wafted through the room, making all of them sit up and take notice. McKay's voice came over the comm. at the same time.

"Environmental systems are back on and functioning. We should have heat, water, and power to all areas. I've blocked off the unoccupied parts of the city for now until everything here in the habitat area is cleared. Then we can start them up in sections, in case there was any further damage caused during the submersion. I've started a diagnostic on the stargate; it should take about thirty minutes to run. Are there any MREs on the jumper?" Sheppard perked up at that question and turned questioning eyes to the others. Ronon nodded when it appeared no one else knew.

"The full kit's there. I did that part of the check list." He said succinctly. Sheppard was up out of his chair in an instant and running for the door. They could hear him yelling something at McKay, who yelled something back. By the time the others had gotten to the door Sheppard had disappeared down the back stairs and McKay was headed out the main doors at a fast clip. He was yelling something as he went, but as he was not using his radio they could not catch it. They exchanged glances. Beckett sighed and started to follow at a slower pace.

"I'd better go and make sure the silly gits don't founder themselves on the MREs. Or kill each other trying to get to them first. I'll be taking them both down to the infirmary to give them complete physicals when I can drag them away from the food." Teyla and Ronon went as well, and Elizabeth was left with Caldwell. She looked at him.

"Well Colonel, we have a definite statement from the man concerned, clear evidence that he definitely hasn't manipulated the city to his own comfort, and we will have Carson's test results as well. I am prepared to tell the SGC and the IOA that the Trust made a mistake, that they must have either misinterpreted their source information or they did not take into account the difference in physiologies between ancients and ourselves. Will you do the same?" Caldwell considered for several minutes. She knew he did not like John Sheppard, both professionally and personally. He did not feel that John was the man for the job, nor did he think much of the younger man's personality. Despite that, Caldwell was a fair man, and he had every evidence that the Trust had been wrong. If anyone should be happy to hear that it should be him. He finally nodded.

"I agree, pending the results of Dr Beckett's tests." She nodded her thanks with a smile and started down to the gate room. McKay had said that it would take a half hour for the diagnostic to run on the gate system, and she found herself drawn to go and see how Rodney and John were. She decided not to fight it. Soon everyone would be coming back, and the city would be busy once more. She would be back at her job, and aside from the no doubt dry reports that they both would file; she probably would never know everything that had happened. The whole thing would become part of the Pegasus galaxy experience and fade away. For now though she wanted to spend a little time with John and Rodney, simply to see them. Caldwell must have seen her purpose and he sat down in the chair in front of Rodney's computer. "I'll stay here and keep an eye on things. I need to speak to my ship anyway." He knew he would not be particularly welcome in the casual circumstances that would be prevailing.

She made her way to the infirmary, slightly unsettled to be moving through an empty city. She went through the doors and was happy to feel the warmth that seemed to have built up here. She followed the noise to find McKay sitting on an infirmary bed talking to Ronon and Teyla. The scientist was eating the entrée portion of an MRE and had two other packages lying on the bed next to him. He finished the one as she came up to the bed, and he tossed it aside to open another.

"A little nippish today Rodney?" she asked.

"You try making do on emergency rations and filet of what could possibly be the universes' ugliest and most bony fish, and see how you feel after two weeks. The Athosian surprise from the first year would be a welcome dish about now." Everyone but Ronon scowled at the thought of the goulash like food the kitchen had produced in the first year when supplies had been short. No one had like that particular dish, even McKay.

"Carson is doing the tests on John?"

"Yes, Dr Weir." Teyla said. "He said that due to the nature of the tests he needed to have the colonel in a quiet area with no interruptions." Her eyes slid to McKay and then away.

"You know how it is Elizabeth. When you call the spirits all the portents have to be just right. Carson wanted to rattle his beads in quiet. All the better for me, I got the MREs." He smirked. She noticed that he hadn't opened the last MRE however, and she happened to notice that it was one of the turkey sandwich ones of which John was so fond. She patted McKay's shoulder and tugged at his beard.

"Will we be seeing the end of this, or are you going to start a new trend among the scientists?" She asked. He shook his head.

"It comes off as soon as my razor gets here from the mainland. I would have done it with one of your Lady Schick safety razors, but I have very sensitive skin, and didn't want to live with the razor burn. Besides, it kept my face warm." She ignored the fact that he had obviously been in her bathroom, she could not begrudge them any comforts that they had found. He must have read her mind as he reached for the pocket of the parka he had shed. He pulled out a small notebook and handed it to her. The first few pages were filled with John's neat printing, listing items and where they were taken from. She flipped through, and saw that the last pages were in McKay's less legible hand. They had noted every item taken, and if it could be returned or not. Most of what was noted was some type of food, though she noted a few other things such as her own blanket and a bottle of Midol. The blanket was marked for return. The Midol was not. She also caught sight of several books, a handheld soduku game, and, strangely, a battery powered nail buffer. She wasn't sure she wanted to know about that one.

"I'll pay for the stuff that we used. There's not really all that much to any one person, just a lot of little stuff from a bunch of folks. John was pretty thorough when he went through the first time." He looked very unhappy for a moment, as if remembering something, and he absently patted the remaining MRE. "He was starving to death you know." He said suddenly. "When I got here he was starving to death. He couldn't get to the areas where the fish were able to get in, that area had been locked down until about two weeks ago. He was surviving on those damn emergency rations, if you could call it surviving. He said he didn't want to tell us because we'd worry. Idiot." She slipped the booklet into her own pocket. If anyone wanted reimbursement she would take care of it herself.

In another twenty minutes Carson and John returned. She thought that Carson looked slightly unsettled, but she put it down to the condition of his patient. John was down to his long john shirt, and they were all treated to yet another reminder of his thinness. McKay's lips tightened, and he waved the MRE at Sheppard who took it and sat on the bed next to McKay and started eating. His restrained nibbling as compared to McKay's high speed scarfing was noticeable. As he ate the team was chatting about what had happened in the time they had been apart. She noticed that John's eyes kept drifting toward the door, and she finally had to ask.

"Who are you waiting for?"

"Caldwell and the marine escort to take me back to Earth." He said baldly. "Unless of course they are just gonna throw me through the gate so they can get at me quicker."

"That's not going to happen, John. We've seen that you and the city seem to be unaffected, and you've given your word. I assume that Carson's tests didn't show anything to the contrary since he hasn't said anything." She lifted an eyebrow at the doctor and he shook his head. She gave Sheppard a gentle smile and patted his knee. "I'm afraid you're stuck with us." He gave her a shy smile in return. She was about to ask about how they had kept busy when Caldwell's voice came over the comm.

"Dr. McKay, your laptop is saying your diagnostic is completed." He announced. Rodney popped off the bed in a rush.

"Don't touch anything!" He snapped into his own radio as he headed out the door.

"Wouldn't dream of it, Doctor." Caldwell replied dryly. Sheppard was sliding off the bed, crumpling the now empty MRE package.

"Guess this means we can get the kids back. Should we go and keep Rodney and Caldwell from coming to blows?" He started toward the door.

"Colonel-" Beckett began. Sheppard turned and gave him a look. The doctor sighed. "All right. Do what you have to do, but I want you back here when you are done and plan to spend the night. I want you to take a course of IV antibiotics to see if we can get rid of the last of the fluid in your lungs and I want to give you some concentrated vitamins and minerals to start building your system back up. Your immune system is going to be weakened, and you'll be susceptible to every bug that's out there. Your isolation has been a help to you there, but you'll not be isolated much longer. You don't want a cold on top of the rest of it." Sheppard nodded and headed out the door with his remaining teammates. Elizabeth paused and looked at the doctor.

"Is he really all right, Carson? He's so…" She didn't finish the obvious. The doctor nodded.

"Aye, nothing that a lot of good meals and some antibiotics won't put right. I would suggest some psychological assessment, but I know that would go over like a lead balloon. We'll just keep an eye on him for the next wee bit. He'll be back to his normal good health in no time. Rodney will help with that. You can't beat the man when it comes to food."

"Rodney's okay as well then?"

"Oh aye. That silly bugger needed to lose a few pounds anyway, and I guess they had to walk everywhere with the transporters out so he got some exercise on top of cutting back on the calories. All in all he's doing better than he was before he got stuck here." Elizabeth shared his smile and headed toward the gate room, leaving the doctor to putter around in his long-missed infirmary.

The next day things were quite a bit busier everywhere when she made her way back to the infirmary. People were moving around even more than usual as everyone was settling back in. Supplies were being moved back into place, and the personnel seemed to be reacquainting themselves with Atlantis. Caldwell had returned to the Daedalus several minutes ago, and they were preparing the data burst for Earth. She wanted to get Carson's data and get it all done. As she entered she almost ran into John Sheppard making a hasty exit, he was still pulling his jacket into place as he was going out. He was back in his regular black uniform, pistol strapped to his leg and radio in his ear. He had shaved off the beard, and while his face appeared thinner, he seemed almost normal. He grinned at Elizabeth, but didn't stop his rush out the door. She turned to watch him rush down the corridor, dodging marines with boxes of medical supplies and scientists rushing around then went on into the infirmary. She was halfway to Carson's office when she heard a strangled cry of anger from the back corner of the infirmary.

"Where the hell has the skirly git gotten off to? Who was assigned to watch him this morning, you Haskins? I told you he'd make a break for it if you weren't watching every second. I'll never get this vitamin injection into him now. He'll avoid me like a bloody wraith. How'd he get his clothes anyway? I thought I banned his team from the infirmary last night." The last question was thrown over his shoulder as Beckett emerged form behind the screens that had been set up to give the back bed a little privacy. The doctor was looking slightly hassled, but she was used to that when one of the SGA-1 team had been in residence. Evidently Sheppard had released himself from the infirmary as per usual, and the doctor was not happy.

"Another prison break, Carson?" she asked. Beckett rolled his eyes.

"I'd take it personally, but I know he'd do it to whoever was in charge." He led her into the office. "What can I do for you? More aspirin?"

"No, I think we finally got past the headache stage sometime last night after all the supplies were through and the last of the security teams had come home. We're finally all here and all is right with the world, at least for now."

"Aye. It's good to be home."

"I came for your test results on the colonel. We're sending the data burst in about twenty minutes and we need to get it compressed and added." Beckett nodded and handed her a memory stick.

"Sorry. We were so busy getting everything resituated I forgot to get it to you. Everything is there. That should satisfy them. I've included the colonel's last test results from his annual physical. They'll be able to see that there has been no change. This whole thing with the trust was just a stupid waste of time that could have ended with the death of a good man. How many times are they going to try to attack us?"

'The G'ould are desperate to regain their dominancy, Carson, and they know what we know, that the Ancient technology is the way to do it. I'm afraid they'll keep trying."

"Well, I am glad this is all over. We all need to get back to normal." Elizabeth tossed the memory stick in her hand, and laughed as she headed toward the door.

"I'm not sure we are ever 'normal', Carson, but I agree 100." It would be good to put an end to this whole thing.

Chapter 18-

SGA-1 was sitting on the western balcony that Sheppard had used to contact the outside. The scrolling sign had been returned to the Geology lab, and the light stick debris had been cleared away. Sheppard's drawing of 'Wilson' was still on the wall, though there were several pails of water and some rags sitting on the floor in front of it, a justification for the team's presence here in the middle of the day.

In fact they were lounging against the wall, looking out over the railing at the blue waters stirring restless below. The breeze was warm and ruffled their hair. It had been a week since the city had risen, and things were getting back to normal. Everything was back in place, and the personnel were settling back into the routine. The Athosians had gotten their homes rebuilt and were also settled in and getting ready to plant their crops. Teyla had returned from the mainland only a few hours ago, having been there most of the week. Sheppard had gotten a hair cut, and both he and Rodney were clean shaven and Sheppard had even had an opportunity to spend a little time in the sun, giving himself a little bit of color in his still thin face.

Everyone was determined to make the man eat, and he was practically overwhelmed with snacks appearing at his door or in his office, or even occasionally in his pockets. He suspected Ronon was to blame for the last, but he still hadn't caught the ex-runner at it. He had outright protested the night before when McKay had insisted on adding items to his tray, and the scientist had promised to back off, though the power bar that had landed in his lap as soon as they sat down indicated that it was not over yet.

Beckett had finally managed to track Sheppard down the week before and had given him his vitamin shot, and had forced a bottle of the same on him that he was monitoring daily. Since the things were like horse pills and tasted like something the horse would produce, they were being diligently flushed daily. All in all he was feeling better. Once they were all back on Atlantis he and McKay had agreed that it was time to bring their teammates in on their secret.

"So, you and Atlantis are more closely joined than before, and you will be able to access more of the Ancient's data base than ever before, but you have withheld this information from Dr Weir and the SGC because you fear that they will take you away if they knew.'

"Not just fear." McKay said. "They would have hauled his skinny butt back to Earth and practically imprisoned him at area 51 or possibly the Antarctic base. He wouldn't have been allowed to stay here in any event. But otherwise you have it right." Sheppard nodded.

"No one will take you if you don't want to go, Sheppard. I promise you that." Ronon said with a glare around as if expecting someone to leap out and try to drag Sheppard off. The colonel waved it off.

"I appreciate the thought, Chewie, but even you couldn't fight off all the marines, at least not all at once. If the SGC decided I was what the Trust said I was, they would order me home, and make me go if I didn't obey. That's why we convinced the city to be slightly more covert in the connection. I've gotten pretty good at the interface thing, doesn't knock me off my feet anymore when the download starts, and I'm careful about talking to the avatar when someone can overhear. Don't need any rumors about me talking to thin air."

"This avatar looks like your mother?" Teyla asked. She understood why they were leery about sharing this information with the others. She had seen how the people on Earth did not understand what was needed here in the Pegasus Galaxy, and would make what she considered bad decisions. Any decision that removed John Sheppard from Atlantis was a bad one. She was grateful that Sheppard considered she and Ronon as being safe to share this secret with. She was however curious about the avatar that both Sheppard and McKay described. She smiled slightly as she saw the colonel's cheeks redden and heard Rodney laugh. She gave the scientist what Sheppard called the 'evil eye' and he stifled the laughter quickly. Sheppard gave her a grateful look and nodded.

"The system was created to join with the children of the builders as they matured. They evidently found that having the avatar in the image of the mother or father was the best way to get the child to actively participate in the process." He explained with a slap at McKay's shoulder when a snort escaped the scientist. "Knock it off, McKay, or maybe we'll discuss a certain someone's attempt at a pedicure." McKay's laughter died quickly, replaced with a petulant glare.

"I thought we agreed not to speak of that?"

"No, you agreed. I just listened to you rant about buffing stones and grinding stones and cheap manicure kits." Sheppard looked away from the now pouting scientist and looked at Ronon and Teyla. "We wanted you two to know. We might run into things when we go to other Ancient sites. They'll sense the enhanced connection and won't be so circumspect as Atlantis is. As it is we're gonna leak out what information we can under the guise of Rodney finally finding the right algorithm to access more of the database. That way we should be able to get what needs to be revealed, but not let anyone know how we know it. Not much will change for us as a team. Just back to the same old, same old, trying to survive in the Pegasus Galaxy, making new friends and enemies, trying to explain why Rodney knows about buffing stones-"

"Oh that is just fine!" McKay yelled and they were off. The snark was flying fast and furious as Ronon and Teyla leaned back against the wall and listened, not understanding more than a portion of the argument.

"Yes," Teyla thought. "Back to the same old, same old, and how happy I am that it is so."

The End.