Elizabeth still wasn't sure what had just happened and the fact that Rodney was just as stumped as she was made her even more concerned. But she could worry about that later; right now she needed to focus on cleaning up the aftermath of the battle. While Rodney, Carson and their staffs had made it through with losing only a few the same couldn't be said for the military contingent.

But such was the way of war, there were always bound to be casualties.

Cautiously stepping on the broken glass that littered the floor of the Control Room, she made her way up the stairs towards her office. Suddenly there was a loud wheezing sound and an unknown wind picked up. Everyone paused what they were doing and looked around for the source of the noise, then Elizabeth thought she dimly saw the outline of a box. Thinking it was just a trick her mind was playing, Weir blinked rapidly but the outline didn't go away; in fact it was growing more and more solid.

Still aware that there were still unknown threats out there, John and his men aimed and loaded their weapons at the area the box was occupying. No one spoke as the wheezing came to an end and the box filled out. Elizabeth could feel the tension in the room as everyone waited to see what new danger was behind the doors, but at the same time she had a nagging feeling in the back of her head that the box was familiar.

Then it clicked just as the door opened and the Doctor stuck his head out. "John." Elizabeth said as she made her way down the steps. "It's alright."

John recognized the Doctor once he stuck his head out but at the same time didn't back down; it was his fault that those things had attacked the city. Only when Elizabeth all but ordered him to lower his weapon did he signal his men to do the same.

The Doctor smiled as everyone relaxed and stopped looking like they were going to shoot him if he looked cross-eyed at anyone. Fully stepping out of the TARDIS, the Time Lord said in his normal care-free voice, "Nothing like a good stand off to get the hearts beating but still...better when those things aren't pointed at me."

Elizabeth looked at the mysterious man for a few seconds, trying to understand how he could be so happy when people had just died defending the city. "I think we need to talk." She finally said.

"Of course, wouldn't dream of leaving without a little chat. Would be terribly rude." The Doctor said as he heard Martha step out. Glancing at her, he asked a silent question and she gave her head a slight shake. Pretending like nothing had happened, he took a step towards Elizabeth while saying, "Why don't we go to your office, we can talk there before we get to the clean up."

"So the Ancients built a fail-safe in case the Dalek's tried to turn on their creators?" Elizabeth asked slightly skeptical. Even knowing that Pegasus was filled with things she couldn't begin to understand, she was having trouble believing what the Doctor had just told her.

The Doctor nodded his head while folding his arms, "Both here and at the outpost."

"But I've never seen anything like you've described on the maps or even a mention in the database."

"That's because they didn't want it known to the general public, only those who built it knew about it and there might be some mention of it in the database; you just haven't stumbled across it."

"Where is it?" Elizabeth asked as she pulled up a map of the city and gave it to the Doctor.

He studied it for a few minutes and then pulled up a section of the city that he guessed they hadn't even gotten around to exploring, "Should be there."

Elizabeth looked at the area and made a note to have John take Rodney and some of their people down there; they needed to see if the fail-safe could work again if the need arose.

However there was one question that still bothered her, "How do you know all of this? From what you told me it all happened so quickly."

"That it did, but I figured out that there was some kind of weapon they had made. The Alterians thought they were brilliant but they weren't stupid; some of them had to of known that the Dalek's wouldn't stay compliant forever. And the TARDIS filled in the rest, turns out the old girl was talking to the city the entire time we've been here."

"I thought that Time Lord and Ancient technology weren't compatible."

"Oh they aren't. But the TARDIS has been around for awhile; wouldn't surprise me if she still had a few tricks up her sleeves."

Elizabeth couldn't help but smile at the Doctor's choice of words. But the amusement was short lived because they had a lot of work to do in the months ahead. It wasn't going to be easy but the Expedition would carry on as it had done from the beginning. She stood and was going to thank the Doctor for his help when the sounds of a commotion were heard.

Walking out of the office, Elizabeth went to the walkway and looked out over the Control Room to see the Doctor's box disappear.

Jack inhaled deeply and coughed violently as he choked on the air that entered his lungs. He was dimly aware of movement besides him, of arms holding him as he shook the cobwebs of death away. After what seemed like an eternity the coughing subsided and Jack opened his eyes to see Martha's face.

Halfheartedly smiling he managed to say, "I knew an angel was watching over me."

Martha chuckled at the comment while giving him a smack on the arm.

"Ow," Jack winced, pretending to be hurt by the blow. "what was that for?"

"For dying on me. Don't you know that you're not allowed to do that?" Martha said with a smile, although her eyes were serous.

"Sorry, although I wasn't planning on it." Jack said as he slowly sat up and looked around to see that he was in the TARDIS. "How long?"

"Almost two hours." Martha replied, standing and moving towards the glass of water she had set out a few hours ago. Getting it, she then went back to Jack and gave it to him. "Drink this, but slowly."

"Thanks." The cool liquid felt good against Jack's parched throat and as he handed the glass back to Martha, Jack realized that there was something off about all of this. It wasn't the fact that he had almost no idea of how he got back to the TARDIS or even what had happened back at the outpost...it was something else.

Something that was bugging him and he didn't like it.

Martha noticed the troubled look on Jack's face and asked, "What's wrong?"

"I don't know...feels like I forgot something."

"Forgot like 'I think I left the stove on' or forgot like 'I completely forgot the fact that it was our anniversary'?"

"A little of both, I think." Jack stared at Martha for a few minutes, hoping to come up with what was bothering him but he was still at a loss. Shaking his head, he gave her a smile and started to stand, "Don't worry about it, I'm sure that it'll come to mind."

Martha reached out to help Jack up when the sound of the column activating reached her ears and she paused, wondering what was going on.

The sounds stopped as suddenly as it had started and the pair stood still, waiting for the next shoe to drop. But nothing happened and Jack knew that one of them would have to poke their head outside in order to see what was going on.

And since they had no idea what was out there it would have to be him.

Slowly making his way towards the door Jack felt Martha grab his arm. Pausing he didn't say anything, having his look do all the talking for him.

Martha knew that look, she'd seen it plenty of times on the trips she'd taken with Jack and the Doctor however he'd only come back to life a number of minutes ago; she was sure that he didn't want to repeat the process so soon. But at the same time she knew that it was useless to convince him otherwise.

"Fine, but I'm coming with."

Jack just gave her a smile and continued towards the door. Opening it, he stuck his head out and took in the surroundings. Where ever they were it looked like it had been through hell; debris everywhere, machines crushed under pieces of metal, glass shards strewn all over the place. Taking a few hesitant steps, he caught a glimpse out of a window and saw spires that looked very much like the ones on Atlantis. Then he saw the main tower and realized that they were still on Atlantis; although where they were Jack had no idea.

Looking around, he realized that this place must have been some kind of lab; but why the TARDIS had brought them here he had no idea. Being mindful of the glass on the floor, Jack slowly made his way inwards. The nagging feeling kept getting stronger and while he would admit that something in this room was responsible for it, he was at a loss as to what.

Martha watched Jack thread his way through the debris, wondering what was on his mind. She didn't ask because he might get distracted and hurt himself and she didn't want that to happen, but it looked like he was looking for something. Not sure what to make of it, she just stood there; waiting for some kind of answer.

Minutes passed and the feeling hadn't gone away but Jack was ready to give up. Maybe it was just his imagination that there was something here, a side affect of coming back to life. Turning around, he looked at Martha and said, "There's nothing here."

"Then why'd the TARDIS bring us here?"

Jack shrugged, "Got me. But let's get out of here." He took a step forwards when he thought he heard something. Pausing he listened but there was silence. Dismissing it, he took a few more steps and was about to take another when he through he heard something again. Stopping, he waited to hear the noise again.

"What's..." Martha started to ask but trailed off when Jack raised his finger to his lips in order to shush her.

"Listen." He said quietly, eyes wondering around the room; looking for anything out of the ordinary.

Then he heard it; a faint groan. Quickly glancing at Martha, Jack could tell she had heard it as well. But they had no idea where it was coming from.

Both of them waited to hear it again and after a few seconds they did, this time it was accompanied with the sounds of debris being moved. It was coming from Jack's left and so that was the direction he moved in; being careful not to hurt himself he searched for signs of life.

"Hello?" Martha called out as she moved into the room, trying to get whoever was in there to respond so they could find them easier. "Can you hear me?" There was no reply and Martha feared that they had arrived too late. But then they heard another groan, this one louder than before.

Narrowing the area, Jack continued to look for any signs of movement. Then he saw something out of the corner of his eye and stopped, turning towards where he thought he saw it.

The hand stood out, it was so covered in blood and grime that it almost made Jack recoil in horror. There was no way that the owner of the hand was alive. But until he saw for himself that they were dead Jack would try to keep an optimistic outlook.

"Over here Martha!" Jack called out as he started to clear the area. It was going to take two in order to remove the larger pieces of metal that had collapsed on top of the person. Once they had gotten the easier sections removed, Jack saw that there was more than one hand; which meant that there were two people under there. Although who they were he had no idea; the groaning had stopped and Jack hoped that they weren't too late.

After what seemed like hours, they were finally making a dent onto the pile that had encompassed whoever it was under it. Lifting a rather large piece, it must have shifted some things around because all of a sudden there was a small avalanche of debris. Not wanting to hurt the people trapped, Jack and Martha moved their bodies over the ones on the ground and waited until the shower was over to brush themselves off.

Removing the last bit of glass from her jacket, Martha and Jack then removed the final pieces of metal and were finally able to see the owner of the hand that they had found.

"Oh my God!" Martha gasped when she saw who it was.

"What just happened?" Elizabeth asked the Doctor, who had followed her out of the office.

The Doctor stared at the spot where the TARDIS had been, "I haven't the faintest clue."

Weir looked at the man and while she found it hard to believe that he had no idea what was going on could see from his expression that he was telling the truth up front for once. She could also tell that it worried the Doctor but didn't know what to say. However, before she could say anything the Doctor brightened up and said, "Never mind that, I'm sure she'll come back when the time's right."

Moving so that he stood by Weir at the balcony, the Doctor said, "There's a lot to clean up."

"That there is, more than we can see." Elizabeth replied in an even tone. "It'll take time, but I'm sure that the city will sparkle once again."

The Doctor chuckled, "Well if they have you at the helm I have no doubt that it will." He then started down the steps, eager to join in the clean up.

Elizabeth watched him go and couldn't help but wonder, yet again, who he really was. It seemed like one moment he had the weight of the entire universe on his shoulders and then the next he was as carefree as a bluebird. She was sure that there was more to the man than met the eye but at the same time he had helped save the city so she wasn't going to go looking for answers; if he wanted to clear the air then she would be more than willing listen.

Realizing that she had to get back to work, Elizabeth made her way down to Chuck's station and asked, "Where's Doctor McKay?"

"Down by the ZedPM ma'am." Chuck replied looking up at Weir. "Wanted to see how much energy was left."

"Good, let me know when he reports in."

"Yes ma'am."

She then headed down the last flight of stairs in order to head over to the infirmary and talk with Carson as to how many injured and dead there were. Elizabeth knew that there had to be a long list and she hoped that most of them were injured; it would be near devastating to the military force here if there were only a few survivors.

Elizabeth had almost reached the door when the familiar wheezing sound and rush of air appeared. Pausing, she was surprised that the TARDIS had returned so soon; it had only been gone a few minutes. But then she remembered that it traveled through time so for all she knew was that it had been gone for hours.

Everyone had paused what they were doing when the sounds appeared, those standing closest had moved out of the way; not wanting to be caught in the wake of the ship's arrival. After it had finished appearing no one moved, waiting for the door to open once more and its occupants to exit.

The door opened almost immediately and Elizabeth saw Martha appear; supporting someone. It was too much weight for her and she collapsed to the ground, being careful not to drop who she was helping.

Martha hit the ground while at the same time made sure that Lorne wasn't hurt even more by her fall. She then sat up and she tore at Evan's shirt where it was ripped. What she saw was bad; there were bruises and gashes everywhere, but what worried her most was the long tear on his side as well as the nasty looking cut on his head. It was a miracle that he was still alive.

Not caring about what people would think of her, Martha was a doctor and when it came down to modesty or saving someone's life it was easy as to which one was chosen (and she was wearing a cotton undershirt), she took off her shirt and pressed it against the long tear on Evan's side.

Looking up for the first time since the had arrived, Martha saw that everyone was looking at them with a measure of surprise in their faces; like they didn't know what to think of what they saw. However before she could look for the Doctor her attention was attracted towards the hallway as Carson and some of his staff came running into the room.

Martha kept the pressure on Lorne's side while Carson stopped and knelt down on the opposite side. Not missing a beat she said, "Jack and I found him under some rubble and he's had trauma to his head and side. I have no idea how long the Major was under everything so we need to act fast." She moved away when one of Carson's staff took over holding her shirt to the wound but continued talking, "He's lost a lot of blood and has been unresponsive since we found him."

"How did you then? Looks like he's been buried for awhile." Carson asked, noting the caked blood on the Major's forehead as they got ready to transfer him to the stretcher.

"We heard someone groan and it was him." Martha replied as they moved him onto the stretcher and then started to move out of the room. Knowing that she'd be more help with Doctor Beckett than here with all the techs, Martha followed them as they moved.

She then heard the familiar creak of the TARDIS door and paused; looking at the Doctor as she did.

The Doctor looked towards Martha as she left and saw her pause, looking back towards him. Then he saw the pain flash across her face, but then she turned away and was gone.

Wondering what that was all about, the Doctor turned his attention to the TARDIS where the door was opening. Knowing that it was Jack, it had to be since him and Martha left together, he smiled knowing that his friend was alive and ready to start the task of setting everything back to rights.

The door opened and Jack appeared, with him the smile slowly fading from the Doctor's face.

He was holding Max in his arms.