Beckett stood next to Sheppard, checking his pulse. He was sitting on a chair. When the Doctor let his wrist go, Sheppard looked up at him.

"You have to do something, Carson. I can't keep this up."

"I know, Son." Beckett said softly.

"Neither can the City." McKay pointed out even as he watched his friend lower his head in exhaustion. "These disruptions are causing all kinds of problems. We've already had some…"

"Yes, Rodney." Beckett glared at him. He looked back at Sheppard. "It's just too risky."

"What about the stasis chamber?" Elizabeth suggested.

"It won't work." McKay responded first.

"Since the chamber will only put him in stasis, when we bring him out of it, the enzyme and protein will still be in his system." Beckett paused, his expression grim. "Besides, I am not willing to put even a healthy person in that thing. We just don't know enough about it yet."

"We could fly over to the mainland." Ronon spoke for the first time.

"Can you imagine what would happen if he shut it down?" McKay dismissed the idea with a shudder. He looked at Sheppard. "Now that we know what's happening, can't you just stop it?"

Sheppard looked up at McKay with an unreadable expression. McKay finally looked away.

"Sorry." The astrophysicist was contrite.

"I can go to the Alpha site."

"Out of the question." Beckett said as a lab technician walked up and handed him a datapad. The young woman whispered in his ear then left. He tapped on the pad and read the screen.

McKay moved close enough to look over Beckett's shoulder. Everyone except Sheppard showed interest in what the Doctor was reading. He was pacing again and barely glanced over.

Beckett exhaled. "All of the drugs we have tested have serious contra-indications with the combination of the enzyme, protein and the chemical. Even the mildest sedative would probably be fatal."

"Then he should go to the Alpha site." McKay interrupted.

"I now have enough data on the rate John's system is able to rid itself of the substance. It's a slow process, about the same rate as it takes for the human body to clean out the enzyme itself. I estimate about another thirty-six. It's been thirty-six hours since the Wraith…" Beckett frowned as he watched Sheppard. "It's not going to be easy, Son. I'm sorry."

Sheppard looked around at the others. He stopped walking, but could not seem to stay still. Elizabeth was reminded of the way McKay behaved after he escaped Ford's men. One big difference, however, was Sheppard's coherence. He was bouncing off the walls, but still made sense despite the chaos going on in his mind.

"Carson, I can't stay here. At the rate it's going, I could shut down the entire City long before this stuff if out of my system. I have to go to the Alpha site." He started pacing again. They could all see and hear his desperation.

"John." Elizabeth bit her lip.

"Lorne's back and the Daedalus will be here in two days."

Teyla turned to Beckett. "Ronon and I will stay with him again, Carson."

Ronon nodded agreement. "We'll keep an eye on him."

"I'm not happy with this, but, okay. I'm coming, too." Beckett looked at Elizabeth. "If that's alright with you."

Elizabeth watched Sheppard as she thought. A moment later, she nodded. "I want regular reports."

"We will meet you in the Gate Room as quickly as possible." Teyla said to Beckett, then she and Ronon escorted Sheppard out.

"I'll get back to work." McKay pointed to the door and left.

Beckett stopped Elizabeth as she moved to follow. He held up the datapad. "There's something you need to know."

"What is it?" Her concern was growing.

"I have no idea if there will be any long lasting affects or what they might be." He held up a hand when she started to talk. "Rodney, Teyla and Ronon were very lucky the addictive effects of the enzyme were short-lived and that there were no other side-effects. This is a whole new thing."

She thought for a moment. "Does John know?"

"He's the one who brought it up to me." He squeezed her arm, hoping to reassure her and himself. "John is one of the strongest people I know, Elizabeth. I'm sure he'll come through this."

Elizabeth nodded. She heard the uncertainty in Beckett's voice but appreciated the effort. "I hope so."

----------

Thirty minutes later, Beckett, Teyla, Ronon and Sheppard waited at the edge of the Gate Room floor. Ronon carried his own bag as well as a backpack. He scowled when Sheppard tried to relieve him of the pack. They were all dressed for going off-world. A team of Marines, also ready to go off-world, stood nearby.

McKay approached. He looked at Sheppard with an apologetic expression. "Sorry, I wish I was going with you, but we're going to be checking out all of the systems here for a couple of days. You've made a bit of a mess."

The ghost of a smile appeared on Sheppard's face at McKay's attempt at humor. "It's okay, Rodney. Sorry."

"I'll go up and dial the Gate for you." McKay nodded and turned away just as Elizabeth walked up. He climbed the stairs to operations.

"Do you have everything you need?" She looked from Sheppard to Beckett and back again.

"I think so, yes." Beckett answered as he watched Sheppard. He saw the Colonel slowly stop moving. His downcast eyes began to go out of focus. Beckett looked up to McKay and mouthed 'now'. The astrophysicist began the dialing sequence. "We have to go now."

Sheppard spoke in a low, strained voice. "Ronon."

Without hesitation, Ronon pulled his weapon and fired it at his friend. Before anyone could move to catch him, Sheppard fell to the floor.

"What the hell are you doing?" Beckett dropped his bag and knelt next to his patient. He tapped his transceiver. "Medical team to the Gate Room!"

Teyla glared at Ronon as she knelt, too.

"What have you done?" Elizabeth almost shouted.

"Sheppard told me to shoot him if he started to…" Ronon wiggled his fingers in the air. He went pale as he dropped his bag and Sheppard's pack. "He said he'd talked to you about it, Doc."

Beckett felt for a pulse at Sheppard's carotid artery and lifted both of his eyelids. "Of all the stupid, insane…He did not talk to me about it."

"Carson?" Elizabeth hovered over the Doctor's shoulder.

"He's breathing and has a pulse, not much of one, but it's there." Beckett looked over his shoulder to the corridor leading to the infirmary. "What the bloody hell was he thinking?"

McKay stopped the dialing sequence and ran down the stairs. He stared at Ronon. "What's going on? Why did you shoot him?"

Before anyone could answer, the gurney arrived. Ronon swept Teyla aside, scooped Sheppard up and laid him on it. Beckett hurried off with Sheppard, infirmary personnel at either end of the gurney. The others followed close behind. Ronon brought up the rear, his face dark and brooding.

----------

Kate Heightmeyer looked around. She had come to see if Sheppard was alright and found Elizabeth and his team waiting to hear if he would live at all. The discussion so far was mostly one-sided, hers.

"Our memories are two dimensional copies of the real events of our lives. As time passes, our minds filter out more and more of the fear and pain we feel. Even good memories lose some of the stronger feelings after a while. The details are still there. We just don't remember them." She crooked her fingers to indicate quotation marks with the last sentence.

McKay shook his head. "How does that explain that he can shut down the City?"

"John is living periods of his life as if it were the first time all over again, as if they were the events themselves. He hasn't talked much about the memories he is actually experiencing, has he?" She looked around at them.

"Other than to say that he was remembering the Wraith feeding on him when some of the blackouts occurred, no, he hasn't said anything specific." Elizabeth answered.

"I believe that he has been experiencing good memories, but it is probably safe to say that many instances have been very bad ones. I'm not surprised that the events of the day before yesterday have been very close to the surface. They would induce extremely strong feelings."

"And, with the ATA gene…" McKay waved one hand in circles.

They fell silent.

"I'm sorry, if you do not need me here, I have…" Kate stood up. She understood that they were not in the mood to talk with her there, if it all. Weariness from lack of sleep and worry for Sheppard had made them retreat into their own worlds. Perhaps if she left, everything they were feeling right now would allow them to open up to each other. Group therapy was quite possible without her.

"Yes, of course, you have work to do." Elizabeth nodded. "Thank you."

The psychologist nodded and left the infirmary.

Elizabeth watched Ronon, who had turned away as Kate spoke.

"Ronon, no one is blaming you." Elizabeth tried to get through the Satedan's black mood.

"I don't understand why you had to shoot him." McKay looked at him with disbelief.

"Sheppard told me…" Ronon stopped and hung his head for a moment, visibly upset. "He said he couldn't risk shutting down the Gate or Ops."

McKay shrugged and nodded. "Well, there is that."

They waited for Beckett to finish whatever it was that needed to be done. Each was reminded of another time when they had waited for news of their friend. Each retreated into the memory and the feelings it provoked. Each was painfully jerked out of their thoughts when Beckett entered the room.

"Your weapon has only two settings, right? If set on stun, it generally renders a person unconscious for just a few minutes?" The Doctor asked Ronon.

"Yeah. Sheppard should have come around after five, ten minutes at most." Ronon's frown deepened. "What's wrong?"

Beckett held up a hand. "Don't go try taking all the blame, Son. Col. Sheppard had more than a little to do with it."

"What's wrong?" Ronon asked again.

"He's still unconscious." Beckett held up both hands to stop the questions the four people in front of him began to ask. "And, I don't know why."

"Do you have any idea when he'll come around?" McKay asked.

"I'm sorry, no. Look, it's almost dark. There is nothing you can do here. Go get something to eat and some rest." When they didn't move, the Doctor put his hands on his hips. "I can make that an order if I need to. When he regains consciousness, or if there is any change in his condition, I will call you. Now, go."

----------

"I need to eat before I go back to getting this City working again." McKay observed as they left the infirmary. He glanced at his watch then looked at Elizabeth, Teyla and Ronon. "Anyone fancy some, well, early dinner?"

"I do not feel hungry just now, Rodney." Teyla shook her head.

Realizing that he did not want to be alone with his thoughts, McKay almost whined. "Aw, come on. You need to eat something."

"Well, I could use some tea." Elizabeth agreed.

They were soon sitting around a table in the corner of a sparsely populated mess. Anyone coming in did not approach their table. McKay and Ronon had meals in front of them. Elizabeth and Teyla sipped on mugs of tea.

"Look, I can't help it if I'm hypoglycemic. He's eating, too." McKay pointed his fork at Ronon as he defended his heaping plate of food. He seemingly failed to notice that Ronon was only pushing his food around with a fork.

"Yes, Rodney. We understand." Elizabeth said wearily. "I just said that I wasn't hungry, that's all."

Ronon cleared his throat and looked at the others. His voice was rough. "I'm sorry. I never would have fired on Sheppard if I knew it would do this."

"Ronon, you don't need to apologize." Elizabeth sympathized. She was the last person who could criticize him. Her inability to trade Ladon for Sheppard had directly contributed to the situation. Sheppard's willingness to dismiss her guilt did not mean that she could forgive herself. "John was right, and you did the right thing."

"He did?" McKay nearly choked.

She glared at him then looked back at Ronon. "Yes. There was, and is, a real danger that John could shut down the Gate or Ops, or both."

"Do you think you can bring the City's systems back now?" Teyla asked.

McKay hurriedly swallowed. "Who knows? I still don't understand what Sheppard did or how he was able to do it."

"We know he doesn't need to be in actual contact with the Ancient technology to control it." Elizabeth pointed out.

"Yes, but he usually needs to be in close proximity." McKay explained. "He at least needs to be in the same room. He's been manipulating systems all over Atlantis today, yesterday, whatever. And, the fact that he's been doing it without conscious effort is more than a little frightening."

"Yes, it is." Elizabeth set her mug on the table. Her eyes narrowed in thought. "It's also fascinating that John can affect so much of the City without being in contact with an ATA sensor, or even near one."

McKay dropped his fork and leaned back. "Yeah."

----------

"Carson?" Franks knocked on Beckett's door then poked his head in. Beckett's head was resting on folded arms on his desk. He was sound asleep. Franks winced, not wanting to wake him. He reluctantly shook the sleeping man's shoulder. "Carson."

Beckett jerked awake. He blinked and rubbed his face with both hands. 'Yes? What's wrong?"

"It's Col. Sheppard. You'd better come look at him." Franks backed out of the office as Beckett stood up.

"What is it, Greg?" Beckett rushed past Franks and into Sheppard's room. He was relieved that he had been able to have a naquadah generator assigned to the infirmary for emergency power. "When did this happen?"

Sheppard's eyes were open. They were not focused on anything in the room, but moved restlessly as if he was watching something far away. Beckett passed his hand in front of them. There was no sign of recognition or of Sheppard even noticing it.

"We think just a few minutes ago." Franks went to the other side of the bed. "James was taking vitals and logging them into the computer. He saw Col. Sheppard was awake when he turned back. There's has been no reaction, though."

"Thank you." Beckett nodded. He looked down at Sheppard. "John? Can you hear me?"

He waited a moment, then pulled out his penlight and carefully flicked the light across Sheppard's eyes. Beckett was relieved to see the pupils react, but was disappointed the man did not. The eyes still darted here and there. Beckett wished he knew what was going on inside his friend's mind.

"John?" Beckett firmly rubbed his knuckles up and down Sheppard's sternum, careful to avoid the Wraith's feeding site. There was still no reaction. "Col. Sheppard?"

Beckett straightened. He looked at the EEG readout. It had started with delta waves when they brought him back from the Gate Room hours earlier. Slowly, the waves had changed to theta and alpha to beta. Beckett would have normally expected him to waken with that change, but Sheppard remained unresponsive. Beta waves dominated the record for the last hour.

He stood beside the bed, not knowing what to do next. Several minutes later, Beckett was suddenly aware that Sheppard's breathing was slowing. As he watched, the restless eyes suddenly stopped moving and closed. Beckett looked at the monitors. Everything registered within normal ranges for someone at rest.

----------

"It's the entire City. Only the naquadah generators and Earth-based equipment are working." McKay groaned as he leaned back in the chair. He looked up at Elizabeth. "We can't do anything. We have to reinitialize every Ancient system, and we won't be able to do that until Sheppard stops doing whatever he is doing. If he wakes up."

"Rodney." She frowned at him in the lantern light. "You can't turn anything on?"

"You think I haven't tried?" He put his hand on an ATA sensor to prove the point. Nothing happened. "Oh, this is so not good."

----------

"Bloody hell." Beckett looked around. Something was different. There was a sudden tangible silence and stillness that unsettled him. He checked the monitors then his patient. Nothing was happening that indicated Sheppard was in distress.

The nurse walked in. "Looks like everything is out now, Doctor."

"Thank you, Connie." Beckett tapped his transceiver. "Dr. McKay, this is Beckett. What's going on?"

McKay's exasperated voice responded. "The whole of Atlantis is out, Carson. Everything. What is Sheppard doing?"

"He's asleep, Rodney." Beckett looked at Sheppard as he spoke, worried that the Colonel wasn't just asleep. He glanced at the EEG readout. It indicated near dreamless sleep. Beckett, however, wasn't really sure.

"Well, can you wake him up?" McKay's voice was strained.

"No, Rodney, I cannot." Beckett's weariness translated into impatience. "You, and a good number of the people in Atlantis, have the ATA gene. Don't tell me you can't sort this out."

There was a long silence. "Certainly, it would just be nice to know that he's not going to turn it all off again. If you don't mind, let me know when he wakes up."

"Alright, I'll let you know." Beckett sighed and turned off the vox on his transceiver. He rolled aching shoulders and sat down. After watching Sheppard for several minutes, he picked up the datapad containing his medical file and began to read it again. Perhaps there was something in it to help him understand what was going on.

Halfway through the file, Beckett glanced up to see an increase in the activity on the EEG monitor. The wave frequency quickly moved from delta to theta then beta. Beckett turned to watch Sheppard, expecting him to regain consciousness. When nothing happened, Beckett checked the cardiac monitor and sighed. It indicated little change in heart rate.

----------

McKay sipped from his coffee cup and grimaced. He set the cup down and swallowed. "Can't someone at least get me some hot coffee?"

When no-one reacted, he sighed and turned his attention to the console and laptop in front of him.

Everyone froze when the lights in the Gate Room and Ops began to come up. One by one, the consoles and screens powered up. McKay, Zelenka and several technicians pounced on keyboards and controls, anxious to test system functions. Elizabeth impatiently watched from the edge of Ops.

After several minutes, McKay walked over to her. He was blinking wearily, but grinning. "I don't know how, but all systems appear to be coming back on line. So far, those we've been able to check are functioning normally again."

"Sheppard?" Elizabeth asked.

"Maybe. We'll be testing for days, so…" McKay pointed at the Ops consoles.

Elizabeth nodded. "Okay, set up a work schedule and let people get some rest. Including you. I'm going to the infirmary."

"Elizabeth?" McKay stopped her as she turned to leave. "Let me know how he's doing."

"I will."

----------

Beckett entered Sheppard's room to find Elizabeth, Teyla and Ronon waiting with him. "I don't remember saying you could have visitors just yet."

"I distinctly remember you did." Sheppard responded with a straight face.

"Right." Beckett suppressed a smile then became serious. "I want to know precisely what were you thinking, telling Ronon that it was okay for him to shoot you with that damned weapon of his?"

"I thought…"

"Thought what? That was one of the most idiotic bloody stunts I have ever seen!" The Doctor looked away for a moment. "John, it could have easily killed you, and almost did. How did you think it would make Ronon feel if it had?"

Sheppard winced at the tone in Beckett's voice. He looked at Ronon. "Sorry. I guess I wasn't thinking it through, but I couldn't risk shutting the whole place down, Carson."

Beckett relented. "I understand, but it was very wrong of you to ask anyone to do such a thing. And, don't you ever say that I've approved such nonsense again."

Sheppard was suitably apologetic. "Okay."

"What's the verdict?" Elizabeth asked, wanting to change the subject.

"Well, as we thought, the levels of the enzyme, protein and the chemical are significantly lower. Everything seems to be returning to normal." Beckett held his hand up before they could celebrate. "We still don't know if there will be any lasting effects, so don't…"

Sheppard interrupted him. "Doc, I haven't had any episodes for hours. The headache's just about gone, too. I feel fine."

"That's all well and good, but you're going to stay here for another twenty-four hours so that I can be sure." Beckett folded his arms over his chest. "On that note, you need to get some real sleep. We all do."

"I'd like to know something before we go." Elizabeth looked at Beckett, who nodded. She turned to Sheppard. "If you don't mind my asking, what happened that you were able to reverse the shut down? What were you remembering?"

Sheppard frowned and bit his lip. "I don't know. It wasn't…my…memory. It was something that happened here, in Atlantis, but it wasn't me or any of us."

"Maybe it was just a dream or even a hallucination." Beckett suggested. "You'd been awake for more than two days and under enormous stress."

The Colonel shrugged. "I don't think so. It was just as vivid and realistic as any of the memories. It just wasn't one of mine."

The End

Footnote: I've been wanting to do backstory on Sheppard for some time. I'm hoping my attempt at it offers a reasonable insight of how he became who he is.