Chapter 1: Leaving Earth.

Three years earlier.

Earth – San Francisco bay.

The mess hall was a buzz of activity when John entered for breakfast – today was the day that they were heading back to the Pegasus galaxy. The queue was long at the serving table, so he took the time to reflect on his time on Earth.

It had been a long twelve months while the powers that be had battled it out deciding what was to be done about Atlantis. The SGC wanted Atlantis back in the Pegasus galaxy, while the IOA was fighting for them to stay because they thought that Atlantis could best protect Earth from the Wraith on Earth. The SGC along with Woolsey had argued again and again that the best way to stop the wraith from attacking Earth was to stop them from reaching Earth in the first place – for a long time, the president was on the fence. In the end, other nations of the world became nervous that a city as powerful as Atlantis was in American waters and that was the deciding factor.

About a month ago it was decided by the leaders of the world that Atlantis would go back to the Pegasus galaxy to try and stop the Wraith there – something that he'd known all along. He hadn't been involved in the meetings though, so he didn't have a chance to voice his opinion.

There had been a lot of tension between the nations who knew about the stargate program and at times he thought that war may break out – well maybe that was a bit of exaggeration. The biggest problem was some countries wanted to tell the public about the Stargate program. He was glad that in the end common sense prevailed and for the moment the program was kept secret.

Today he couldn't be happier since he would be heading back to the place where he felt he belonged. There was nothing left for him on Earth since he had tried to make amends with his brother, but things hadn't gone too well. As usual, David kept telling him that he should quit the military and come and work for the business because the air force was no place for a Sheppard. They had sent e-mails back and forward for a while after that conversation, but eventually, they'd stopped communicating altogether. At times he wondered if he should try one last time before leaving Earth since he had no idea when – or if – they'd be back.

The Daedalus had picked out a lovely planet for them to land on and Caldwell had even been in touch with the Athosians on a couple of occasions. The news from the Pegasus Galaxy wasn't good though as the wraith were continuing to cull entire worlds, but on the flip side, there was continued in-fighting, and they kept blowing each other up – perhaps the wraith would eventually destroy themselves and they wouldn't have to do anything about it.

Speaking of Wraith, he knew that there was one extremely sick Wraith down in the holding cells that he needed to talk to after breakfast. Jennifer and Carson had been working on a retrovirus so that the wraith didn't have to feed on humans, and they had injected it into Todd months ago. They had given Todd plenty of food to eat, but for some reason, his digestive tract wasn't handling it too well. The doctors told him that Todd would probably die, but he would have died anyway because they didn't have a steady stream of humans for the big wraith to feed on.

One of the good things to come out of their time on Earth was he'd been promoted to Full-Bird Colonel. That had happened two weeks after they had landed, apparently the powers that be had been impressed that he had been willing to take out a Hive ship with a nuke, almost sacrificing his own life in the process. Luckily, his friends had been on board the Hive, so it hadn't come to that. The ceremony was small – much to his relief – with only a few members of the SGC, the President and his team attending.

Four weeks ago, Woolsey had stepped down from the leadership of Atlantis and decided to stay on Earth. At the time he had no idea that they were considering him to take on the role of Atlantis leader, so it came as a complete shock when a week later it was offered to him. He'd taken his time to decide because he didn't know if he wanted that responsibility, but in the end, he'd accepted the role and Lorne was instated as his military commander and 2IC

Finally, he reached the serving table and chose some bacon and eggs, juice, and coffee. Taking a quick survey of the room he noticed that his team were sitting at their favourite table overlooking the Bay. As usual, Dr Jennifer Keller and Amelia Banks had joined them, and Carson was also there.

There was a spring in his step, as he walked over to greet them, "how are you this morning?" He asked them all.

Torren who was seated in a highchair at the end of the table squealed, "Da!"

"I am well, thank you, John," Teyla replied, "I cannot wait to finally get back to New Athos so that I can see Kanaan."

"Who that Momma?" Torren asked and he could sense the kid's confusion.

Although he knew that Teyla had tried to tell Torren about his father on many occasions, she didn't have a picture of him, so how was a young kid supposed to understand?

"He is your Father and I'm sure that he misses you very much."

The kid still looked confused, and John doubted he even remembered Kanaan, he suspected Torren had no idea what a father was either.

"Dad!" Torren exclaimed pointing at him.

Teyla was very quick to answer – perhaps a little too quick in his opinion, "No that is not your father that is Uncle John."

Torren just smiled at him and got back to eating his pancakes. He wasn't sure what to say or do so he changed the subject, "So Ronon, Banks, I hear you're moving in together."

Ronon's answer was short and to the point – as usual, "thinking about it."

Amelia just stared at her food and didn't bother to say anything.

Okay on to the next couple, "Doc, McKay, how are things with you guys?"

"Alright," McKay answered with a mouthful of food.

"They're going well," Jennifer said with a smile that lit up her face.

After that, she fell silent and continued to eat her meal. He had no idea why, but everyone seemed quiet today. A little voice from the end of the table broke the silence and he had to admit he was a little relieved.

"Da wide on sateboard?"

Smiling he thought of how he'd been sitting Torren – or T.J. as he liked to call him – on his board and pushing him down the corridors of Atlantis. Torren was determined to be able to ride a skateboard just like him. He could totally understand why Torren would think of him as his Dad because he had spent so much time with the kid since he was born. Skateboarding, reading bedtime stories to him and he'd even bought T.J. a tricycle for his second birthday.

"Not today buddy, we have to get ready to head back to the Pegasus galaxy today."

Torren nodded his head and he appeared to be thinking, "Our home?"

"Yes, it is our home," Teyla replied. "It is where I grew up and where you were born. It is also where your father is."

He had no idea why Teyla kept bringing Kanaan up every five minutes as she hadn't talked about him in months – perhaps she really loved him. While they'd been on Earth, he had considered making a move on her, but there was no way he could do that if all she wanted to do was get back to New Athos to be with Kanaan again.

"So, Sheppard, have you been on any dates lately?"

He looked up at Ronon, who had a sly grin on his face, and he chose to ignore the question and change the subject.

"So, Carson are you looking forward to heading back to the Pegasus Galaxy."

"Aye, I am Colonel. I can't wait to get back to the work that I started before we ended up on Earth. I'm not looking forward to having to fly the city again though."

"I'm sorry Carson, but I'm going to need to be in the control room coordinating things from there. Lorne will be able to relieve you if need be. Although with the star drive functioning correctly and three full ZPM's it shouldn't take too long to get there."

"How do you feel about taking command Colonel?"

The last thing he wanted to do was discuss his feelings, if he opened up now, he was sure that Carson would send him to see the shrink, "I'm fine with it," he replied using his standard answer.

He was happy when Carson fell silent and didn't bother to press the matter further.

Pushing his plate away, he decided that he wasn't that hungry, "Right, I have to go and see Todd before we leave, apparently he wants to talk to me."

"Aren't you going to eat your food?"

"I'm not hungry at the moment Carson." Carson looked as if he were about to argue, so he thought that he should say something to placate him, "Don't worry doc, I'll grab a muffin and coffee before we leave."

Before anyone else had a chance to say anything he left the table heading to the holding cells and the last thing he heard before he was out of earshot was, "bye Da."

Smiling he left the mess hall and proceeded to the nearest transporter.

Jennifer's latest report on Todd had stated that the Wraith probably wouldn't make it to the Pegasus Galaxy, so he wondered why Todd wanted to speak to him. Did he have a final request before death? Or did he want to blame him for his death somehow? Maybe he wanted a fight to the death, hoping that he would kill him, rather than have to die a slow painful death.

When he arrived, he was surprised to see the Wraith standing up and he looked much better than he had the last time he'd seen him.

"Ah…John Sheppard, it is good to see you looking so well."

He looked at the big Wraith suspiciously, "you look well."

"Yes, I have found in the last few days that your human food has begun to agree with me. I like the pizza and beer in particular."

"That's good to know, but what is it you want to talk to me about?"

"I have a request to make John Sheppard."

"Okay…."

"When we arrive in the Pegasus galaxy you let me go? I would like to contact my hives and see if they are interested in having the treatment to stop them feeding on humans."

"Why?"

"I owe you my life John Sheppard and you are an honourable man who I am happy to call brother. So, if you and I can get along, I am positive that humans and Wraith can work together."

"I'll think about it," he said before turning around and heading towards his quarters

Todd was an enigma, and he couldn't work him out, at times he seemed like an ally and at other times it seemed as if he wanted to hand you over to his wraith friends and let them feed on you. He still didn't trust him, and he wondered if there would come a time when he could.

He had half an hour before he needed to be in the control room, so he decided that he should probably head to his quarters for a shower. But perhaps he needed some time alone before they left Earth for the last time in who knows how long. In the end, he decided to head straight to the control room.

Arriving in the control room he headed straight to his favourite balcony trying to steal a few moments of peace. He knew that the journey would only take a few days, and then the hard part would begin. The first thing that needed to be done when they landed on their new home world would be to get the gate online. Next, they would contact the Athosians and the rest of their allies.

Caldwell had connected with the Athosians when they'd been in the Pegasus galaxy three weeks ago and all seemed to be well – he'd even spoken with Kanaan, leaving Teyla extremely happy to know that he was still alive and waiting for her.

After that who knows, life would go on in whatever form it took.

Teyla had told him that if Kanaan asked her to be bonded with him that she would accept because she wanted to spend the rest of her life with him – whether it be long or short. At the time he'd looked at her with a glazed look on her face and tried to be happy for her.

Sighing he looked at the glistening blue bay with the city of San Francisco in the distance. He had spent a lot of time there over the last year and he wondered if he was going to miss it. Once or twice when Dave was in the city for business, he would have a meal with him and although they were civil to one another things were extremely uncomfortable. He'd even managed to take Teyla and Ronon to the mall on one occasion, Teyla had loved it and wanted to spend all of his money – much to his horror, but Ronon thought it was a nightmare. He never took Teyla to the mall again; she went with Jennifer and Amelia after that.

He chuckled at the memories and continued to look out at the crystal blue bay taking in every sight, every sound, and every smell. He had no idea whether he would ever see Earth again and maybe it made him feel a little sad.

It had been an interesting time and he knew that if he stayed on Earth any longer, he would be bored to death. In fact, he'd probably be asking Todd for a fight to the death himself. He'd spent plenty of time sparring with Ronon and even managed to win once or twice. Teyla was a different matter though; every time she sparred, she'd wear one of her traditional Athosian outfits and it usually took his breath away. He had no chance of winning when she was dressed like that, so in the end, he gave up. Teyla didn't seem to be bothered about it and he guessed that was because she had Kanaan on her mind.

A voice from behind him interrupted his contemplations, "Sir, General O'Neill wants to speak with you before we go."

He turned around to see Chuck Campbell standing at the door, "thanks Chuck, I'll be there in a minute."

Turning back to look at the bay, he wondered again whether he would ever see it again. He knew that if he didn't, it was his choice to leave the planet of his birth.

When he arrived in the control room a few minutes later he found that Teyla and Lorne were there talking to the general, via a video transmission.

"You wanted to talk to me General?" He asked coming up alongside Teyla and Lorne.

"For the next two days you'll be unable to contact the SGC, so I just wanted to check and see how you're feeling."

Great now the General wanted to talk about his emotions, "I'll be fine general, I have a lot of good people here to support me."

"Well in that case Colonel, you have a go. I look forward to hearing from you once you reach the Pegasus Galaxy. Oh… and good luck."

"Thank you, General, Sheppard out."

He turned to look at the people in the control room and they were all standing around waiting for him to issue orders. He was in charge now and these were his people, so taking a deep breath, he started giving instructions.

"Chuck, I want you to monitor the atmospheric conditions as we take off. Amelia, can you keep an eye on the shield and make sure it's holding, Zelenka can you give her a hand with that." He turned to Col Lorne before continuing, "Lorne I want you to go to your quarters and make sure you get plenty of rest so that when Carson needs a break you are ready to take over. And before you argue I know that you haven't had much sleep over the last few days."

He was relieved when Lorne nodded and immediately left the control room, turning to Amelia, he asked her to put him on an open com.

"Attention, everyone. In a few minutes, Atlantis will be leaving Earth and heading for the Pegasus Galaxy once again. For some of you, it will be your first time leaving Earth or travelling into space. We will arrive at our new home, which has been designated F32- 123 in a little over forty-eight hours. Flying the city will be Dr Carson Beckett, who has piloted the city before, Lt Col Evan Lorne will be on standby in case he is needed. There shouldn't be any disruptions to your normal routine, so just go about your usual activities." He paused, before speaking again. "Dr Beckett, Dr McKay you have a go."

At the moment Rodney McKay was down in the chair room monitoring the city's systems as they took flight. Dr Zelenka would relieve him if he needed a break.

Suddenly a loud rumbling sound filled the room, and he knew that the star drive had been activated, rushing to the nearest balcony he and several others watched as the city took off from the bay. There was a huge downdraft as Atlantis rose from the water creating incredibly rough waters. He wondered what anyone watching from the shore would think of it. But it wasn't his problem it was up to the IOA and SGC to deal with the public, all he had to do was make sure Atlantis got to the Pegasus galaxy.

It wasn't long before they left the atmosphere and they were in space once more, a million points of light invaded his senses and he wished that he had time to admire the stars – perhaps later.

Before he had a chance to blink Atlantis had picked up speed and entered hyperspace.

TBC…