I am heading off on holidays with my family, so this will be my last update for at least a week. Enjoy!

Chapter 4: Back on Atlantis.

Shalite walked onto the bridge looking for the captain, because she really needed to talk to him about taking John to visit Atlantis. She had thought about talking to him on more than one occasion over the last couple of days, but for some reason she felt apprehensive about talking to him.

Tuart had certainly given John the cold shoulder since he'd come on board and Shalite sensed that he didn't like him much, she was sure he had his reasons, but he hadn't bothered to tell her.

When they had first met she had been able to talk to Tuart about everything, but since John had come on board things had become a little more difficult. She loved Tuart with all of her heart and was looking forward to having his child, but his reaction to John had been disconcerting to say the least. From the moment she'd woken up this morning, she had made up her mind that she was going to confront him about it this morning, but he had left for his shift before she woke up.

Looking around the bridge she realised that he wasn't on the bridge, she walked up to the second officer and asked him, "do you know where Captain Smith is this morning?" Finding it a little difficult to use his rank, but she was on his ship and she thought that she needed to set a good example for the rest of the passengers and crew.

"He's in his ready room Ma'am." The second officer informed her.

Taking a deep breath, she walked to the small room off the side of the bridge, he spent way too much time in there for her liking, but when he was on the ship, it was his office, so perhaps it was understandable. Once they were home again they would spend so much more time together.

Rubbing her swollen stomach, she pressed the door chime, in around ten weeks' time they would be having their baby and she couldn't be happier. She had fought hard to come on this mission, as the Science academy felt that a pregnant woman was a liability on this mission, but in the end, they had given in to her demands and allowed her to come, then when she found out that it was her husband that was going to be captaining the starship she couldn't be happier; until now.

She heard his voice from the other side of the door. "come in?" He asked and then the door slid open.

Walking into the room, she saw him standing at the window overlooking the planet. He was almost as tall as her when he wasn't slouched and standing at his full height and his hair was pitch black. She walked up alongside of him and hoped that he would turn around and look at her with his bright blue eyes, which she loved so much.

"What can I do for you this morning Shalite?" He asked in a matter of fact tone.

She sensed that his mood wasn't the best this morning, so she knew that she would have to tread carefully with her questions, "I would like to take John down to Atlantis, to have one final look around before we head home?"

"For what purpose?"

Really, she thought. That has to be the dumbest question that Tuart has ever asked. "It was is his home and perhaps he would like to see it one last time." Shalite told him with a roll of her eyes.

"Do you trust him Shalite?"

She was beginning to get annoyed with his line of questioning, so she decided to come straight out and ask him what his problem was, "What is your problem with John Tuart?"

"I know that he is 50,000 years out of his own time period and he wants to get back to his own time."

"So"

"Well have you ever stopped to think that if he goes back to his own time, all of history could be changed?"

She had considered the possibility but hadn't given it a lot of thought, "yes Tuart I realise that is a possibility, but right now all I want to do is to give him the opportunity to see his home one last time. Whether he can go back in time or not is still a question to be answered at another time."

Watching him, she saw that his blue eyes narrowed and she was afraid that he was going to deny her request. She'd actually decided coming in, she would take John to Atlantis no matter what he said.

She was relieved when he finally spoke, "I will grant your request, but I will send Roget along as well, to keep an eye on him."

If she wasn't so annoyed at him, she would have thrown her arms around him, "Thank you Captain," she said without emotion in her voice.

As she left the room, she saw Tuart turn his back on her and stare out of the window. She knew that she would have to talk to him later, but for now she was off to see John and tell him the good news.

OOOOOOOOOOOOOOO

It was two days since he had looked out over his beloved city and today was the day that the doctor had finally deemed him fit enough to be released to quarters.

The rooms he had been given were guest quarters and they were larger than crew quarters. There was a table and chairs in the middle of the room and off to the side there was a room with a queen size bed. The carpet on the floor was thick and grey and there were drapes on the windows, which he decided that he'd prefer open than closed. These quarters were certainly more extravagant than anything he'd ever slept in on the Daedalus.

He had been hoping that he would get to share with someone, but Rodney had been given his own guest quarters, which was totally weird, because he had no idea whether holograms slept or not.

Sitting down at the table he stared at the food which someone had left for him. He hadn't had much of an appetite over the last few days; apparently that was another symptom of hibernation sickness. It looked like some kind of scrambled eggs and bacon. There was a serve of toast and some kind of juice as well. He picked up a piece of the toast and decided that was all he was going to eat for now. Perhaps he'd try some juice as well, but much to his chagrin there was something that was missing; who would eat breakfast without a cup of hot steaming coffee.

When he'd finished his toast, he pushed the rest of the food away and went to get dressed, as today was the day that he was going to set foot on Atlantis again. Well he assumed he was going to visit Atlantis today, but Shalite hadn't bothered to get back to him as yet. Apparently, she had been too busy to speak with Captain Smith, which was probably a lie as she spent most of her spare time with him; they were husband and wife after all.

He picked up the clothes that were on his bed and thankfully they were similar to what he might wear if he was off duty back home. The shirt was made of some kind of blue material similar to cotton and the pants were similar to jeans, they hadn't given him any other shoes, so he just put on his standard issue military boots.

A few minutes later the door chime chimed, and he automatically thought open, but of course nothing happened. He certainly missed being able to do that and he had every intention of trying to communicate with Atlantis once they were in the city.

He walked over to door and he was happy to see that Rodney was standing outside, "Rodney come in, I've just finished eating breakfast."

"I wish I could eat," Rodney whined, "because although I have the ability to touch objects now without my hand passing right through them, I still can't eat."

John couldn't help laugh at the thought of a hologram trying to eat, but he had other things on his mind, so he didn't dwell on that thought, "has Shalite told you what's happening this morning?"

"No, I haven't heard from her as yet." Rodney replied looking glum.

"You know what Rodney? I think I will go whether she wants to help me or not. I don't think her husband trusts me, so I'm pretty sure he's going to say no." John said with determination in his voice.

Rodney sighed and John could sense some pearl of wisdom coming his way. He was finding it hard to get used to this Rodney, because he was so much softer than the man he once knew.

"Think of it from his point of view, if you go back in time and change the timeline, the whole of history could be changed." Rodney explained to him gently.

"Yeah, but won't this reality continue on as an alternate timeline?" John asked feeling a little confused; he really hated temporal mechanics.

"Yes, I know that, and you seem to comprehend it, but not everyone is as smart as us."

Wow did McKay just call me smart? I'll have to tuck that away for another time, was the first thought that crossed his mind once Rodney had finished speaking.

He was about to offer a smart comeback when the com device that had been inserted into his arm activated.

He tapped his arm and was surprised to find that Shalite was contacting him,

"Sheppard here."

"John, the Captain has given you permission to come to Atlantis with us, can you please meet me on the bridge in twenty minutes, to be transported down to the planet?"

"I'll see you then and thanks Shalite."

"You're welcome John and can you tell Dr McKay that he can come as well."

"Sure thing, we'll see you in twenty minutes, Sheppard out."

Once he had finished the communication, he found that Rodney was sitting at the table looking at his left-over food. John wondered if he was going to start eating it or not. Not saying anything he just stood and watched for a few minutes before speaking, "Come on Rodney, there'll be plenty of time to try eating later."

Rodney looked up from what he was doing, "and where are we going?"

"We're off to Atlantis."

"Captain Smith agreed then?"

"Yeah, and I'm sure he wasn't happy about it," John smirked before dragging Rodney through the door and towards the bridge.

If this was the last chance he was going to get to see his city again, he was going to make the most of it. They were nearing the bridge when he thought of something that he had meant to ask Rodney, so he stopped and looked around to make sure that no-one else was about.

"Hey McKay, do you think that Atlantis could ever fly again?"

"Well, I don't see why not, are you thinking what I think your thinking?" Rodney asked with a gleam in his eye, something that he hadn't seen in a long time.

"I sure am, so can you come with me to the chair room, then you can look at the systems and I can try and communicate with Atlantis?"

"Sounds like a plan," old McKay replied and John was delighted that he was beginning to remind him of his long dead friend.

They entered the bridge together and found that Roget and Sharlite were waiting by the view screen, "John, Rodney are you ready to go? "Captain Smith asked and walked up to them with a suspicious look on his face.

John nodded and walked up to Shalite and stood next to her. Rodney followed and stood on the other side. He leant in to Shalite and whispered in her ear, "Rodney and I want to go down to the chair room when we get there, do you know where that is?"

Before she had a chance to answer him, he felt the transporter beam envelope him and the bridge of the Phoenix disappeared to be replaced by the control room of Atlantis. When the transporter beam dissipated, he turned to look at the stargate. It looked haunted in the eerie red glow of the red giant, the view gave him a strange sense of foreboding and he had no desire to look. It brought him a great sense of anguish, because the last time he was here there was a hope that he would be traveling through it to get home, but for now that wasn't going to happen, so it didn't really bear thinking about it.

Before he had a chance to become too depressed he turned to Shalite, who was busy talking to McKay, "hey Shalite, can Rodney and I go down to the chair room now?"

It was Roget who answered, "I will come with you?"

John just rolled his eyes, of course Roget wanted to come with him and he had a sneaky suspicion that the captain had asked him to keep an eye on him. He was relieved a few seconds later when Shalite saved him form having to tell Roget that he didn't need an escort.

"Don't worry Roget, I will accompany them!" Shalite told him forcefully and it was obvious to John that she wasn't going to take no for an answer.

He sensed that Roget was going to answer back and the last thing he wanted right now was to be the cause of an argument, "I think Rodney and I can manage on our own. Don't worry, there's no way I can go back in time and change history right now, so you can either trust be or throw me in the brig."

"I trust you John and I understand your desire to return home. Perhaps at some point we can talk about what your plans for the future, or the past might be?" Shalite said smirking at him.

"I would love to have that conversation with you, but it will have to wait for another time." He said and smiled at her, she was the one person he'd met in this time period that he actually trusted. He knew that she would at least hear him out, before casting judgment on him.

He nodded at her and grabbed Rodney by the arm, "come on Rodney, let's head down to the chair room and see what we can come up with?"

They headed down the corridor towards the one and only transporter that seemed to be working, luckily for them the use of it would bring them out near the chair room. The corridors were bathed in the same eerie red glow as the gate room and there was a fine layer of red dust covering everything. The fact that he had spent 300 years in stasis in the abandoned and dreary place filled him with a real sense of hopelessness.

"Hey McKay is there anyway for us to use the gate to get back to my time?"

"If we move Atlantis, the solar flare I was predicting will not be able to interact with the gate in the same way, but if we don't move Atlantis it really won't matter anyway. If we are able to move Atlantis we may be able to calculate when another Solar Flare will interact with the gate, but the odds of it sending you back to your time are astronomical. I think our only hope is finding a time jumper and hoping that it can travel back 50,000 years. If not I'm sure that we can do some research and try to improve the specs."

"Or a TARDIS?" John smirked.

Rodney chuckled, "do you think anyone had invented one yet, or perhaps someone has actually found a race of Time-lords. Well we can always hope?"

"Thanks Rodney you're a good friend and perhaps we can find a time ship in some secret lab on Atlantis, but the first thing I want to do is see if we can move the city."

"John I just need to ask, why do you want to move the city?"

"Really I thought that you would understand, the real Rodney McKay would." He said and immediately regretted it, because despite the fact that the man beside him was a hologram, he was one of the few people he could rely on in the situation he was stuck in.

"I'm not the real Rodney McKay and perhaps he would have understood, but I'm not quite sure why you want to do it. Is it for you, or Atlantis, or is it for these people who you barely know?"

"I'm sorry, if I upset you, but I feel as if I need to move Atlantis for posterity's sake, whether you like the ancients or not, they were the ones who first seeded this galaxy and the milky way, so I would like it to stand as a monument to what can be accomplished. I know that a lot of their actions were questionable, but they did a lot of good too."

"Okay John now I understand and believe it or not I agree with you," he paused and rubbed his eyes before continuing, "and you don't need to apologise to me, I'm a hologram remember."

John wondered whether holograms had feelings or not, but perhaps that was a question for another time.

They walked on in silence for another ten minutes and finally they made it to the chair room. John was amazed that he could hear Atlantis whispering in the back of his mind as he approached the room, and that alone gave him hope that they would be able to move her.

The doors opened and the lights came on as he approached and the first thing he did was rush to the control chair in the centre of the room.

"Hang on Sheppard, we need to make sure that there is nothing wrong with it before you sit down in it." Rodney warned him.

John shrugged and sat down anyway, "what could possibly go wrong, I don't think anyone has been in here for Millenia. I guess the worst that could happen could be that it doesn't work."

Sitting in the chair he instantly felt Atlantis humming in the back of his mind, but she sounded different somehow, it was almost as if she was unwell and looking for help.

"McKay something is wrong with Atlantis, I am going to lay back in the chair and see if I can access some of her data files. Hopefully we should be able to get a console or two up and running to do a diagnostic on her systems."

He lay back and closed his eyes enjoying the hum of his city even though it felt a little different to how he remembered it; finally, his thoughts were connected to hers again.

Atlantis are you alight?

It's good to hear from you again John Sheppard. Where have you been for so many millennia?

It is a long story, but we would like to know if you can fly again. Do you have enough power?

I am unsure, I will bring up a display on the monitor over there and you can run some diagnostics on my power systems.

John lay back and continued to feel Atlantis' steady hum and to his relief it seemed to be growing in strength again. He was relieved to find that he still felt as connected to her as he had the day he left to go and look for Teyla, right before the accident that had landed him 50,000 in the future.

John I sense someone approaching and it is one with wraith DNA, not unlike your friend Teyla.

That comment surprised him, he knew of no-one with wraith DNA, really, I don't know anyone in this time with wraith DNA. Perhaps you are mistaken?

I am not mistaken John Sheppard, perhaps she is a descendant of you friend.

That comment really upset John, so he took a few deep breaths before reaching out to Atlantis again with his mind. Teyla died 50,000 years ago and she didn't have any children, so I have no idea what you are sensing.

Another thought struck him, from what holographic McKay had told him, Michael had taken her son for his experiments, he tried to communicate that to her, although I believe she had a son and he was kidnapped by Michael. I honestly don't know what happened to him.

I am sorry John Sheppard, but how can it be 50,000 years since you were last here. Have your people invented time travel? I know the ones you call the ancients were experimenting with it.

No we humans haven't invented time travel as yet, at least not that I'm aware of.

Perhaps you should go and talk to your holographic friend now, because he is waiting for you. I look forward to communicating with you again soon John Sheppard.

Yeah I'll catch you later Atlantis.

John slowly became aware of what was happening in the chair room, when he finally managed to sit up, he felt exhausted. That was always a side effect of him connecting with Atlantis.

Looking around the room he saw that Shalite was standing next to Rodney. He wondered whether that was who Atlantis meant when she said that she detected someone with wraith DNA approaching. Taking a good look at her, he could certainly see how someone could mistake her for being a descendant of Teyla, but unfortunately to his knowledge that just wasn't true. Perhaps some of the Athosians survived being captured by Michael though and she was a descendant of them. He wondered how many other races survived the great-war, maybe there were a few Genii out there somewhere, or even better would be a few Satedans running around, he realised that there was only a few of Ronon's people left when he last saw him, but just maybe…

A voice interrupted his contemplation, "Hey Sheppard, are you listening to me?"

"Yes Rodney I can hear you? But can you please repeat what you just said?"

"I said that there should be enough power in the ZedPM for one trip and I have found a reference to a lab on another planet where the ancients were making ZedPm's."

"Really Rodney, how come you never found that information 50,000 years ago?"

"I have absolutely no idea, but for now, it means we can move Atlantis and find more power so the people in this time can live in the city."

"What does all that mean?" Shalite asked joining the conversation.

John took a deep breath and smiled at her, "It means that we should be able to move Atlantis to a new home and find enough power to keep her systems running, so that the city will be liveable again."

"Are you able to fly the city John, I thought that only a person with ancient DNA could fly it?"

He just shrugged and smiled at her not really wanting to give her that kind of information just yet.

"Wow this is far more wonderful than I could ever imagine, I must tell Tuart right away. Thank you John, Thank you Rodney."

John watched her walk away, he had a feeling that Tuart wasn't going to like their plan to move and power up the city, but he was going to do it anyway.

"So, what do we need to do to get her moving again Rodney?"

"There are a few damaged systems, but I should be able to fix them fairly quickly and then I will search for a suitable planet and we can set about moving her."

"This is great Rodney, thank you for taking my suggestion seriously."

"You're welcome John, now if you can just shut-up and stay out of my way, I will get started."

He smiled at his holographic friend; this was turning out to be an enjoyable adventure. After moving Atlantis there was still one other thing that he had to do and he knew that he had to do it. He had to find a way to go back in time and change history.

OOOOOOOOOOOOOOO

Sharlite was walking down a dark passage way which had strange tendrils growing on the walls, she had no idea where she was or why she was here, but the place seemed vaguely familiar. It reminded her of the holo-images she had seen from around the time of the great war. It was just like a wraith ship.

She continued on in silence unable to speak or make a sound, her whole body was shaking and she was afraid. She had no idea what she was going to find, but still she kept going.

There was someone up ahead and she wondered if they might be able to tell her where she was or what was going on, so she picked up her pace and continued to walk towards her goal.

She arrived at the place where the person was standing and tapped him on the shoulder, when she turned around she was horrified at the half human, half wraith staring back at her.

A strange voice permeated the silence. "ah, Shalite I'm so glad that we finally get a chance to meet."

Finally, she found her voice and screamed…

She awoke with a start to find that there was sweat dripping down her face and she was breathing so heavily that she thought she'd run a marathon. Looking around she realised that Tuart wasn't in bed with her and she started to panic. What had happened to him, had someone taken him? She had no idea what the time was, but one thing she did know was that she didn't want to go back to sleep, because she never wanted to see that face again. She was sure that it was just a nightmare, but still it was very unnerving.

Looking at the clock on her bedside table she realised that Tuart had probably already started his shift on the bridge. She decided that it was probably a good idea for her to get up and start the day and the first thing she was going to do after breakfast was talk to John Sheppard about her nightmare.

TBC…

What is going on with poor Shalite.