Chapter 25: Epilogue.

Twelve months later.

John stood on the balcony overlooking San Francisco bay. They had been on earth for two weeks now and in that time, he had been promoted to Colonel, received The Medal of Honour, and been bored out of his brain. Woolsey was busy most days, talking to the IOA and stargate command and all he had to do was keep Rodney and Zelenka from killing each other and stop Ronon from injuring the new Marines.

This San Francisco was certainly different to the one that he had visited in the future, there were no flying cars for one thing. Putting his hand in his pocket he pulled out the photo that Shalite had given him of her, her son and him together, he wondered what had happened to her in the future. He chuckled to himself when he realised that she hadn't even been born yet and she wouldn't be for another 50,000 years.

At lot had happened since he had returned to Atlantis. In the end he had rescued Teyla, but not before a building had collapsed on him, and a piece of rebar had impaled him through the side. Even after he had been transported out of the rubble, he had still gone on a rescue mission to Michael's hive ship to rescue Teyla, even though he was severely injured. She had given birth on the hive ship, with Rodney helping her out, so in their escape he'd had a chance to hold Teyla's newborn son, Torren John.

Michael had escaped at that time, and they didn't see him again until a few months later when he infiltrated Atlantis and tried to take Torren away from Teyla. They had eventually regained control of Atlantis and John had pursued Michael onto the roof of the city where a fight had ensued. Michael had beaten him senseless, before Teyla had come and finished him off, by pushing his fingers off of the railing he was hanging on to and then he had plunged to his death. At least they assumed he had because a body had never been found.

After his body was healed from the piece of rebar that had impaled him when Michaels compound had fallen on him, Jennifer's consciousness had been inhabited by a wraith like compound, which began to take over Atlantis. It turned out that she had been infected while rescuing him from Michael's compound, as had he and everyone else who'd been in that compound. Carson did find a cure for the pathogen, but it hadn't been tested, so he had volunteered to test it, which had led to seizures and his heart stopping, but the cure worked, he was able to administer it to Jennifer. In doing so he had to crash a jumper through the wall of a tower, and he was impaled by one of the wraith like tentacles, leading to another few weeks off his feet. The only good thing to come out of that situation was that Jennifer had found a way to cure Carson and bring him out of stasis. Carson had returned to earth after operating on him, removing the alien tentacle. Now he had matching scars on either side of his abdomen.

Things went from bad to worse in the Pegasus galaxy, they came across and alternate version of the Daedalus and found that another Rodney McKay had been experimenting with an alternate reality drive and they almost got stuck in an alternate reality for the rest of their lives. They had came across some of Michael's hybrids and had to fight them in a zombie like fog. They had found one of Janus' ancient labs when Dr Daniel Jackson had come to Atlantis, which activated a beacon on a device known as the attero device, which a rogue group of Asgard known as the Vanir intercepted, leading them to kidnap Rodney and Daniel to convince them to activate the device, . They managed to activate it which led to any wraith ship trying to enter hyperspace being destroyed, with an unforeseen side effect; Stargates exploding.

John was in the gate room when an energy cascade started in the gate thanks to the attero device being activated, so they came up with the idea to place the city's shield around the gate to control it. He'd ordered everyone to get out of the gate room and he had stayed with Zelenka to finish the work. In the end the gate had exploded showering him with glass and debris, which became imbedded in his back. Giving him more scars to add to his collection.

There were a lot of other things that went on, but the event that lead them here was possibly the scariest, as the wraith had made it to earth with the help of some stolen ZPM's. He had almost blown himself up by arming a nuke, which he had flown to the hive ship in orbit. Luckily, his team had been on board and they had been able to rescue him. The hive ship had been destroyed and Carson had landed Atlantis in the middle of San Francisco bay.

When he had come back to his own time, he had prayed for and easier time of it, but of course that hadn't happened for him. Not that things had been easy for the others either.

His thoughts drifted to Teyla, who had left her partner Kanaan, along with her entire people in the Pegasus galaxy. Kanaan was also the father of Torren and as much as he didn't like the idea, he knew that he needed to do whatever it took to get her back there and he knew that he would have to speak to her, as soon as he could find her, because for some reason she seemed to be ignoring him at the moment.

He stood and stared at the picture in his hand for a bit longer before heading for the door, he had every intention of finding Teyla and talking to her right of way. If she needed to get back to Kanaan he wouldn't stand in her way, although he desperately wanted to tell her how he thought about her, but he knew what she wanted was the most important thing right now.

He had barely made it off of the balcony when he was enveloped by a transporter beam and he had no idea what was going on. Who the hell would want to transport him of a balcony from a city sitting in the middle of San Francisco bay on earth?

The transporter beam dissipated, and he found himself standing in a small room on a spaceship. It looked like something from the future that he'd visited, but why would it be here, unless… Looking around the room his eyes settled on a woman and it was someone that he thought he would never see again, "Shalite," he whispered.

"John it is so good to see you again!" she exclaimed, running up to him, hugging him and kissing him on the cheek.

When she finally pulled back, he stood taking her in, she was exactly the same as he remembered her, but she looked ten to fifteen years older. "What…how...? He asked, not taking his eyes off of her.

"It's a long story if you come with me, I'll explain everything, have you eaten yet, because we were just about to have something to eat?"

"I could eat." He answered her and he was happy to see her again, but it freaked him out a little at how much older she seemed to be.

OOOOOOOOOOOOOOO

Rodney sat down at a table in the mess hall. He'd waited fifteen years for this day, and he was definitely feeling a little excited. It wasn't long before Carson and Joe joined him.

"How are you feeling Rodney?" Joe asked sitting down next to him with a tray full of food.

"I've got to admit to feeling a little nervous. I can't believe that after fifteen years, I will finally be able to see John again."

"And you have to admit that telling him that rescuing Teyla has made a difference to the future of this timeline, will make a huge difference to him," Carson answered him with a smile on his face.

"I can't wait to tell him what we've been up to over the last fifteen years, I bet he'll be surprised," Joe commented.

"I think the thing that will surprise him the most will be the fact that we're all fifteen years older, although you haven't changed since the day he left." Carson told Rodney, with a smile crossing his worn face.

Carson's right, he thought to himself, I still look the same age as I did fifteen years ago, and I'll probably look exactly the same way when my friends die.

The thought took an edge off of his excitement, as much as he loved his friends, he knew that one day they wouldn't be there, and he would have to make new friends. He hadn't given it much thought in the early days, but now that they had finally managed to find John again, it came back to him as to what he was.

OOOOOOOOOOOOOOO

John followed Shalite through the halls of the ship and he still had no words to describe how he was feeling. Seeing Shalite again had brought back so many emotions good and bad. She had obviously aged and was probably closer to his own age than she had been last time he'd seen her, so how had that happened. Had they discovered time travel?

"Where are we heading Shalite?"

"There is someone I want you to meet before we head off to lunch."

A smile lit up his face, he had a fair idea who that was going to be, but he didn't say anything, as he wanted to let Shalite share her surprise with him.

They walked on for another few minutes before they came to a room. Shalite opened the door and allowed him to enter first, and the first thing that he saw, was a boy of about fifteen sitting in a chair and he was the splitting image of Shalite and when he looked up at him, he could see that he had the same bright blue eyes as his father Tuart.

"John," he whispered.

"Yes John, this is my son." Shalite answered him.

"Wow!" he exclaimed, "he's all grown up."

"I turn fifteen next month," the boy answered.

Shalite looked at her son, "John this is the man I named you after."

"It's a pleasure meet you Mr Sheppard, Mother, Uncle Carson, Uncle Rodney and Joe have told me so much about you."

"Call me John, and believe me when I say the pleasure is all mine," He turned towards Shalite before continuing, "Why is everyone so old? Have you discovered time travel, is that what this is a time machine?" The words tumbled out of his mouth and he was desperate for an explanation.

Shalite took his hand and stroked his cheek and he found himself enjoying the closeness, "I will explain everything over lunch."

John turned to look at his name sake and he could see a smile cross his face, "what?"

"Nothing John, I'm just remembering how much Mom talks about you."

Before John had a chance to answer, Shalite interrupted, "come on let's go to lunch and I will explain everything."

A few minutes later they entered the mess hall and John was surprised to find that Carson, Joe, and Rodney were all sitting at the table. Joe and Carson looked older and Rodney looked exactly the same way he'd looked the last time he'd seen him. "Rodney, Joe, Carson it's so good to see you all again, now can someone tell me what the hell is going on?"

Shalite directed him to a seat, "sit down John and I will get some sandwiches and coffee."

He very quickly acquiesced to her command and sat down at the table and stared at Rodney.

Rodney stared back, before talking to him, "John it is so good to see you again, you have no idea how much I've missed you."

"I've missed you too buddy, even though I've had a McKay on Atlantis with me, he isn't the same as you." He looked at Carson before continuing, "and Carson we managed to use the research you gave us to fix the degradation in our Carson's organs and cells, but I missed you all the same. You too Joe."

Shalite came and put a plate of sandwiches on the table and poured cups of hot steaming coffee for them all, before sitting down.

"Okay, old man McKay isn't it time you told me what the hell is going on?"

"You first John, did you manage to rescue Teyla?"

"Yeah, I did, and she had a son and named him Torren John. We also managed to kill Michael in this time period but shouldn't you guys know that." He thought about what he'd said for a few minutes and then he realised what had happened, "but you're from an alternate reality aren't you, so how would you know what happened in this time line?"

"You're absolutely right, this is humanity's first alternate reality drive." Rodney replied with a huge grin on his face.

He shuddered remembering his own experience with an alternate reality device, "so, you crossed realities and came back in time to come and visit me? Gee I'm touched."

"Really why would I go to all that trouble for a messy haired flyboy like you," Rodney smirked.

"Rodney has spent every day since you left working on this drive," Shalite informed him, "so yes he crossed realities and came back in time to visit you."

John spoke one word and it said everything, "why?"

"Because I wanted to know what happened to you and I wanted to know if you succeeded in your mission." Rodney explained.

"Well I'm fine and yes I succeeded in my mission, Teyla is safe, Michael is dead and we're still battling the wraith, or we would be if the IOA ever let us go back to the Pegasus galaxy."

Joe who had been reasonably quiet until now took that moment to join the conversation. "You know we crossed over to this reality in our time-period."

That comment certainly piqued John's curiosity, "and what did you find?"

"That they never fought the great war, the coalition of planets never lied to their people and," Shalite took a deep breath before she continued, "Tuart is still alive to help raise our son."

"And what happened to Atlantis?" John asked almost afraid of hearing an answer.

It was Carson who supplied the answer, "it was moved by a joint expedition from Earth, the Coalition of planets, and New Sateda and many people went to live and work there."

John looked at the half-eaten sandwich on his plate, it was certainly good news that his mission had been a success, "I do have one question, did you guys ever find out why President Jones wanted me to hide the time-jumper, since by me going back in time I changed the time-line, so the president in this time-line never would have known what I had done with it anyway? Am I making any sense?"

"Not really, all he said to us is that people should not take time travel lightly, so the less people who knew that it was possible the better. I actually don't think the people of this timeline ever found that jumper," Rodney explained to him with a pained look on his face.

All this talk of time travel and alternate realities was giving him a headache, he hated temporal mechanics, but he had to wonder what had happened to his friends in the last fifteen years? "What has happened in your reality? He asked looking up at Rodney.

Rodney launched into a long-winded explanation, "the Coalition of planets did agree to sit down with New Sateda and Earth, and New Sateda was able to broker a peace treaty with The Coalition. After about a year with Earth, New Sateda and the coalition working together, we revealed the location of Atlantis and a Joint expedition was sent to live and work there. Shalite was the leader and Joe and I also were part of it. Even Carson came eventually, after spending some time on earth."

John nodded and looked across the table at Shalite and he noticed her holding Joe's hand, "and what happened to you Shalite, did you ever remarry?" He asked her.

"Yes, Joe and I were married about five years ago and we are both incredibly happy. And what of you John, have you ever told Teyla how you feel about her?"

John blushed that was one of the things on his list of things to do while they were on earth, "Ummm…. It's been a busy year, so I haven't had a chance yet." He decided that this was too uncomfortable, so he decided to change the subject, "did Michael ever show up again?"

"Yes, he infiltrated Atlantis about two years after you left, wanting Shalite's child, but we managed to defeat him and Shalite killed him." Joe told him and John could hear a hint of pride in his voice.

"I don't know whether there is any Michael clones out there, but we haven't seen any sign of it. We came across one or two of his hybrid's in stasis, and we very quickly disposed of them." Shalite explained.

"Yeah, a similar thing happened in our time period, Michael infiltrated Atlantis, tried to take Torren off of Teyla and when we gained control of Atlantis again, Michael beat me senseless and Teyla ended up killing him. We call her Supermom now." John exclaimed with a smile. He couldn't help but smile when he thought of Teyla and Torren, he certainly wished that they were his family and not Kanaan's.

"And what of her husband, is he with you on earth?" Joe asked rather forcefully.

Surely you didn't cross realities to ask me about my love life?" John asked a little defensively," and why is everyone so interested in my love life? What about Carson, let's talk about him. Do you have a girlfriend Carson?"

Carson smiled at him, "Aye lad I do, in fact I met my wife in Scotland over ten years ago and we have been married for seven years and have two children and yes I actually crossed realities to make sure you're alright and that includes you love life."

John sighed and decided that he should probably tell them the truth, "Kanaan decided that he was going to stay in the Pegasus galaxy."

"And have you tried to talk to Teyla about it?" Carson asked with a serious look.

"No, I haven't, I actually think that she's been avoiding me."

"Well find her and talk to her, you deserve every bit of happiness John, you put your life on the line every day so that others can find happiness, don't you think that it's your turn?"

"Thanks Carson, I'll ask her when we get home?"

"Okay then lad, let's enjoy the rest of our lunch and then Shalite has someone she'd like you to meet."

They finished their food in silence and just as they had finished Shalite stood up and headed out of the room. She returned a few minutes later with John and he was holding a girl of about two, she had blonde curls, pale skin, and brown eyes, "this is joe's and my daughter Amelia."

John walked up to his namesake and took the baby off of him, "she's beautiful, just like her mother. I'm so happy for you Shalite, it looks as if you've made a good life for yourself."

"And I want that for you John."

"Thanks, Shalite. I guess I have some down time now that we're stuck on earth, so maybe I'll talk to her."

"The drive is ready to jump realities, so it's time we head home," Rodney explained, "we may never see you again, but I'm glad you succeeded in your mission. I trust that Rodney is happy with Jennifer?"

"You can't separate them. Carson is on earth with us as well and he's thinking of going to Scotland for a visit."

"Well it looks as if everyone is having a good time but you John." Rodney told him with sarcasm.

John looked at his friends and knew that it was time to get home, they'd looked after him when he was in the future, but his family was waiting for him down on Atlantis, that is where he belonged and it was his home.

OOOOOOOOOOOOOOO

Teyla headed out to the balcony overlooking San Francisco bay knowing that was where she would find John.

They had been on earth for two weeks now and she knew that John was bored. Woolsey was tied up with meetings with the IOA and Stargate command and John was left in charge of Atlantis, which meant he didn't have much to do. Rodney and Zelenka were busy fixing Atlantis and Ronon was training the new marines that had come to Atlantis and all John had to do was make sure that no-one killed each other.

It had been a difficult time for her, caring for her son without a partner, but this is where she wanted to be. Atlantis was her home and she had family here, which made it a little bit easier considering that she had left her people behind in the Pegasus galaxy.

And then there was Kanaan the father of her son and one of her dearest friends, but certainly not someone who she would want to be bonded to for the rest of her life. They shared one night together, and Torren was the result, but they both knew that they were never meant to be together. Kanaan had chosen to stay on new Athos, and she had no idea whether she would ever see him again.

That was one of the reasons she was seeking John out, she wanted to know that if anything happened to her, would he be willing to look after and raise Torren. She knew that it would be asking a lot of John, but she could think of no one better to be a father to her son. He certainly spent a lot of time with Torren and Torren seemed to love him. She had no idea whether Torren would ever get to know his biological father, but in John he certainly had someone who was willing to be there for him in every situation.

She remembered the first time she had seen John holding her son. They had just escaped from Michael's hive ship in a dart. He was sitting in the cockpit of the craft gazing down at her son, while he stroked Torren's hair. John was severely injured and barely conscious, but he still held on tight to her son, so much so that when she tried to take Torren from him, he didn't want to let go. It was at that point that she'd decided to name her son after him.

She sighed wondering if things had been different could she and John have been a couple, but she knew that John wasn't interested in her, otherwise he would have told her a long time ago.

She had been putting off talking to him ever since they had arrived on Earth and she knew that she shouldn't put it off any longer, so taking a deep breath she walked out to the balcony and she was happy to find that John was there looking at the bay.

OOOOOOOOOOOOOOO

John felt the transporter beam dissipate and he found himself on the balcony overlooking San Francisco bay again. He knew that he had to speak with Teyla as soon as possible because he was sure she was upset with him. He wondered if he should wait for her to come to him, she always did in the end.

He hadn't seen much of Teyla the last few days either, which upset him, because it was almost as if she was avoiding him. Was she upset because she'd had to leave Kanaan in the Pegasus galaxy? If she were, he swore that he would do whatever he could to get her and Torren back to him.

He thought back to the day that she had told him she was pregnant with Torren. That was probably one of the worst days of his life, because at that point he knew that he had lost her forever. Not that he'd ever had her, so technically he'd never lost her. The first thing he had done when he'd found out, was head down to the lower levels of the city and drink a six pack of beers. He'd then fallen asleep and woken up when Teyla had called him wondering if he wanted to share dinner with her, an invitation that he had promptly refused. She was having another man's baby and she wanted to share a meal with him. That just wasn't on in his opinion.

It took him another two days to find out who the father was, and it was at that point he decided to do everything that he could to support her. The Athosians were missing at, so at the time she really needed him to be a friend and not a judgmental jerk.

Then he'd been transported to the future and he had helped Shalite give birth to another man's baby, sure her husband had been killed by Michael, but he wished that he were watching his own baby being born. Perhaps one day he would get that opportunit

He wondered what would happen to Torren if they never went back to Pegasus. Torren would never know his father. Would Teyla let him assume that role? He knew that he would certainly take on that role if that was what Teyla wanted. He really loved spending time with Torren and at times he imagined that Torren was his son, but then he'd see something of Kanaan in him, so he knew that it wasn't really true.

He sighed and looked out at the bay again, it certainly was a beautiful sight, and he could probably get used to living on earth again. But deep down he knew that he wouldn't be happy on earth long term knowing that the people of the Pegasus galaxy needed Atlantis to help in the fight against the wraith.

He had no idea what he was going to do for the rest of the afternoon, his paperwork was up to date for the fifth straight day and there was no new troops for orientation, so basically other than being on hand if there was an emergency, his time was his own.

It had certainly been an interesting morning, and he was happy that Shalite and the others had moved on with their lives, but he hadn't. Perhaps it was time that he did.

Maybe he would go for a run in the lower levels, since he had nothing else to do for the afternoon, turning around ready to head to his quarters to get changed, he was shocked to see Teyla standing by the door.

"Hey Teyla, what can I do for you?" He asked feeling a little worried about what she might have to say to him.

Teyla was silent and he wondered what was on her mind, he really hoped that she wasn't angry with him for any reason, because that would really suck.

He was relieved when she finally opened her mouth, "John I would really like to speak to you about something important, if you feel that you need to say no to my request I will totally understand, but don't say anything until I have finished talking."

Great, she's missing Kanaan and she wants to talk to me about him, but then she did say she wants to ask me something, so maybe it has nothing to do with him.

Hs thoughts were interrupted when Teyla spoke again, "John did you hear a word that I just said?"

"Sure, I did, you want to speak to me about something."

She looked at him with her serious look, "can we please sit down."

He nodded and led her over to the bench against the wall. Once they had sat down, she took his hand and looked him in the eye. She really looked intense and he was beginning to freak out a little, is she about to tell me that she's dying or something like that?

"John you know that you are my best friend, right?"

Great, she wants to ask me to be part of her bonding ceremony, his overactive imagination thought.

"Yes, you're my best friend as well." He told her knowing that he actually wanted more than friendship, but there was no way that was ever going to happen.

"Well I was wondering whether you would look after Torren and raise him if anything were to happen to me."

Wow I was not expecting that. Was his first thought, but then he thought that it wouldn't matter if they could get back to the Pegasus galaxy, because Torren would have Kanaan.

"Ummm….I would be Ummm... honoured to do that for you, but I promise you that I will get you back to the Pegasus galaxy, so that if anything happened to you, Torren would have Kanaan." He told her with sincerity.

He was totally shocked when she lifted her hand up and touched his cheek, "John I do not wish to go back to Pegasus to be with Kanaan. The only reason I want to go back to Pegasus is to defeat the wraith. My home is on Atlantis and you along with, Rodney and Ronon, Richard, Carson and Jennifer are my family.

He was totally blown away by that piece of news and he didn't quite know what to do with it, so he just opened his mouth and hoped that something intelligible would come out, "So you and Kanaan aren't together. What happened, did he hurt you in any way? If he did, I will beat the crap out of him."

She smiled her gorgeous smile at hm. He absolutely loved her smile, hell he loved everything about her, "No, Kanaan and I are not together and no he didn't hurt me, we are just no longer together." She told him in a gentle voice.

He spoke one word, but it, word was full of meaning, "why?"

"Kanaan and I sought comfort in the arms of each other one night and Torren was the result, but although we both hoped that it would develop into something more, we both decided that it never could because I am in love with another."

Sucking in a deep breath, he realised that her hand was still on his cheek, could she possibly mean that she was in love with him?

"Do I know this person?" He asked apprehensively.

The next thing he knew was that she was leaning towards him and her lips brushed his. He closed his eyes and gently kissed her back.

He was a bit disappointed when she pulled away, "does that answer your question?" she asked, as she leant towards him again.

She kissed him more passionately this time and he was more than happy to respond.

"I love you John I have loved you since the first moment you walked not my tent on Athos all those years ago. I always thought that you were not interested in me, so when Kanaan had showed an interest in me, I was flattered and took him up on his offer."

"I've always loved you Teyla and I was an idiot for not telling you sooner. When you hooked up with Kanaan and became pregnant, I gave up all hope of ever being with you."

"I do not regret having my son, as I love him dearly, but maybe you can be a father to him in Kanaan's absence?" She asked him and he could see the hopeful look in her eyes.

"I would be honoured."

John had no idea what he was going to do for the afternoon when he had walked out onto this balcony, but he certainly had a few ideas now.

"What shall we do for the afternoon Teyla?"

"Shall we go for a walk before dinner? Torren is with Amelia at the moment and she is willing to keep him with her until then." Teyla suggested with her gorgeous smile.

He nodded and grabbed her hand, as they walked of the balcony, he had no idea what the future would hold, but at least he was no longer alone. Shalite and Carson were right he deserved some happiness, but the thing that he never realised was that the happiness he was looking for was right in front of him all of the time.

Fin…

I want to thank everyone who's stuck with this story to the end. Thank you to all of those who have reviewed, I am totally overwhelmed by the support and encouragement for this story, I'm glad that you've enjoyed it. Although I have tried to PM every member who has reviewed, I may have missed someone and for that I am sorry.

I will be going back to finish "Boys' vacation," next, hopefully I'll have another chapter up in the near future.