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Author's Chapter Notes: AN: Here we are; the chapter you've all been waiting for, as John reveals how he came to Atlantis in the first place, which I hope will meet with the approval of all concerned parties…

AN 2: In advance, if anyone wonders why the elder Elizabeth here is capable of walking when she barely had the energy to stay awake for more than a few minutes in canon, I'm assuming that, when the stasis chamber was able to complete the revival process on its own as opposed to the process being controlled by the expedition staff who didn't really know what they were doing, it was able to give her an energy boost that would restore her to a condition where she could operate on her own so long as she wasn't pushed too hard, as opposed to her more vulnerable condition in canon

"What?" Elizabeth said, staring at the old woman in the chamber before her in shock. "She… she's-?"

"She's you?" John said, nodding with a smile that managed to appear rather pleasant despite his face's twisted appearance. "That she is… well, an alternate you, anyway; considering what she told me about her arrival in Atlantis and the circumstances of your own arrival, I'm pretty sure you're never going to become her."

"Oh," Elizabeth said, allowing herself a momentary feeling of relief- after some of the time paradoxes she'd heard about from the SGC, including the reports of how SG-1 discovered Atlantis's previous ZPM, it was good to know that she wasn't condemned to go back in time in the future or something like that-, but then she turned her attention back to the matter at hand. "So… how did you meet her?"

John couldn't entirely believe that this was happening; he'd been dreading this particular turn of events for so long- the idea that someone could be this calm about the mess his face had become wasn't something it was easy to accept after the kind of reactions he'd received in the past-, and now, even after witnessing his response to Teyla and Ronon, Elizabeth was just… standing there…

She had come after him even after seeing him react with violence, and was talking with him as though nothing had changed, even as she saw the face that had driven so many people to attack him no matter what he'd done for them…

Bringing her here might have been an impulsive decision, but, if she was going to trust him after seeing him at his worse, he was going to trust her in return, and that meant telling her the truth.

"I was on holiday with my family…" he began, looking wistfully around the room before he turned back to look at Elizabeth. "I take it you found out more about me back on Earth?"

"I… did some research," Elizabeth replied. "Your father… he's Patrick Sheppard, right?"

"The major utilities guy, yeah," John confirmed, nodding briefly at her as he continued his story. "We were never exactly close when I was a kid, but it just got worse as I got older; by the time we went on that holiday to England, he'd pretty much drawn up my entire future for me without even asking if I wanted any of it."

"Oh," Elizabeth said, looking sympathetically at John.

After so long seeing John as the man willing to save other lives, the idea that he could have ever been regarded as a disappointment by someone, but the pain in his voice as he remembered his father…

He might be trying to conceal it, but Elizabeth had trained to observe the subtle details of human behaviour, and she had spent a fair amount of time with John or thinking about him since they'd first met; it might have been a long time since Patrick Sheppard's son ever felt like he really wanted his father's approval, but it still had to hurt that he'd never received it.

"Anyway," John continued, shrugging dismissively as he continued speaking, "when we were on holiday, my father and I had a bit of an argument- I don't even really remember what about now; some variation on the usual crap about how he wanted me to go into the family business when I wanted to join the Air Force and fly things-, and I stormed off into the woods near our hotel to try and cool down; I managed to outrun my brother when he tried to catch up with me, and ended up walking around the woods for a while, until I… well, I ended up falling into a cave somewhere around there."

"You fell into a cave?" Elizabeth said, surprised at the idea that John could have just found something like that when nobody else had (Actually, on another level, she was surprised to hear about a time when he hadn't been the Phantom; considering everything he'd shown himself to be capable of since she'd met him, it was strange to think about the idea that there'd been a time when he could make that kind of mistake).

"It was a bit off the beaten track, I fell down an embankment when I misjudged the stability of the surface I was walking on… stuff happened and I lucked out on finding a cave nobody knew was there before," John said, shrugging slightly even as he looked wistfully up at the memory. "I'm not sure what happened when I got there- it was dark, I was scared and confused, I only had a short amount of time to look at what I'd found, you know how it is-, but I was staggering along, trying to find a way out that didn't involve climbing back up, when I found some kind of metallic object that glowed blue when I touched it."

"What was it?" Elizabeth asked.

"From what I learned later- and what happened just after I touched it-, well…" John began, before he shrugged and smiled at her. "It was a long-range teleportation device."

"A teleportation device?" Elizabeth repeated in surprise. "The Ancients created something like that?"

"Well, it's not like they went straight from spaceships to Stargates; there'd have to be some intervening steps before they reached that stage," John said, shrugging in a speculative manner at her. "From what I've read over the years and what you've picked up since re-establishing contact with Earth, I'm guessing that it was something Merlin or Moros or whatever you want to call him put together when he was working with the Knights of the Round Table to travel to Atlantis- we weren't staying that far from Glastonbury-, but the end result was that, after being left out in the open for so many years, it… well, it didn't work out well."

"Oh," Elizabeth said, her eyes widening in understanding even before John reached up to scratch slightly at his twisted face. "You mean… that's when… well, your face…?"

"That's when my face ended up like this," John said, nodding in confirmation at her, indicated the twisted mess with a grim smile. "Had a few other off details when I had the time to check myself over- a few internal details shifted around, a bone or two maybe slightly smaller than they were-, but the teleportation system was still intact enough to make sure I survived the transition; it just couldn't put me back together properly, and something in the receiver exploded when I got here anyway."

"Oh," Elizabeth said again, struck by the sheer inadequacy of anything she could say at this point as she reached over to place a sympathetic hand on John's shoulder, still looking warmly at him. "I'm… I'm sorry, John."

"Could have been worse," John said after a brief silence, even if the smile he gave her seemed very obviously forced.

After a moment's silence, he continued. "Anyway, I was looking around the city when I met her…"

John had no idea what had happened to him, but right now he was torn between staring at everything around him in awe and falling to the ground and sobbing with fear.

Wherever he was, it was easily the most incredible place he'd ever seen, beyond any place he'd ever seen or heard of in anything that wasn't a movie or a book, but he just didn't know where he was. One minute he'd been standing in a cave, and now he was running around what appeared to be some kind of vast underwater city, water all around whenever he looked out of a window and the surface far too far away for him to swim up there, never mind that there was no way to know where land was…

"HELLO!" he yelled once more as he ran around a corner, finding himself faced with another empty corridor; his watch seemed to have been just as scrambled by… whatever happened to him… and hadn't worked since he got here, so he had no way of knowing how long he had been running for, and he didn't even know where he was going to go when he got there. He'd been making for the central tower out of a lack of anywhere else to go, but even if he got there, there was no guarantee he'd actually find anyone…

"Hello?" another voice said, responding to his call at last.

"Hello!" John called back, smiling in relief as he ran towards the voice. "Who's there? Are you-?"

As he rounded the corner, his eyes widened in surprise as he saw the source of the voice; an old woman, dressed in a long white robe with hair extending down past her shoulders, her lined face still relatively smooth despite her obvious age.

On the one hand, it was a relief to know that he wasn't going to have to talk to some kind of weird shark-octopus-thing, but that just left him with more questions, particularly since she looked just as confused as he did…

"Uh… hi?" he said, after the two of them had been staring at each other for a few moments in silence.

"Hello," the woman replied, smiling affectionately at him, even if she had a slight hesitance about her manner as she looked uncertainly at his face. "I'm Doctor Elizabeth Weir; who are you?"

"John… John Sheppard," John replied, smiling hesitantly at her. "You… you live here?"

"In a way," Elizabeth said, looking warmly at him. "You're in Atlantis, John."

"Atlantis?" John repeated, eyes widening in surprise as the mythological implications hit him. "As in… the Atlantis? We're under the ocean?"

"We are," Doctor Weir said, still smiling at him before her expression became more apologetic. "It's just… we're not on Earth."

"Pardon?" John said, looking at her in renewed curiosity.

"Well…" Elizabeth said, looking back at him thoughtfully for a moment before she smiled and nodded as though coming to a decision. "I normally wouldn't do this, but considering how far we are from anyone who'll care, I'll give you the full details… as soon as you tell me how you came here."

"I… I just fell into a cave… touched something… it glowed… and, well, here I am," John said, shrugging awkwardly as he looked at her. "I'd tell you more, but-"

"You just touched something and it sent you here?" Elizabeth said, looking curiously at him. "As in, it activated when you came into physical contact with it?"

"Yeah…" John said, looking uncertainly at her. "What does that mean?"

"We'll… talk about that later," Elizabeth said, waving a hand before she looked more firmly at him. "Anyway, to begin at the beginning, Atlantis was actually created by a race known to us as the Ancients."

"A race?" John repeated. "As in… an alien race?"

"Essentially, yes," Elizabeth said. "Actually, the Ancients were the original evolution of the human form, and they developed various incredible technologies over the centuries. They eventually died out- what happened is a complicated story that I'll explain to you later-, but they left most of their technology behind, which we were able to discover later after we evolved to replace them."

"We?" John repeated, looking curiously at her.

"Stargate Command," Elizabeth explained. "One of the Ancients' greatest inventions was the Stargate, a large ring that can create a wormhole allowing them to travel from one world to another; it was discovered on the Giza plateau in 1928, but its purpose was only discovered in 1996 when Egyptologist Doctor Daniel Jackson translated-"

"Hold on; 1996?" John said, looking at her in shock. "But… but it's 1983 back on Earth."

"It is?" Elizabeth said, pausing for a moment before she nodded in understanding. "Well… when I left Earth, it was 2004."

John's eyes widened.

"You're from the future?" he said, looking eagerly at her; an alien city was cool, but time-travel was a different kind of cool (And he'd take anything that gave him a reason not to think about what he was dealing with right now).

"In a roundabout way, yes," Elizabeth said, smiling at him before she looked out at the city before them. "It was a… difficult route… but… well, I was assigned by the SGC to lead an expedition to the city of Atlantis after we discovered an Ancient database that included the city's Stargate address."

"Cool," John said, smiling briefly at her, before he took in the more solemn expression on her face. "So… what happened then?"

"As my expedition arrived, the lights came on, as though the city was sensing our presence," Elizabeth explained. "Unfortunately, even as the city slowly awoke, we only had limited power; the lights were on, but the control consoles were showing no sign that they were drawing on power themselves. While Doctor McKay, our chief scientist, tried to work out a means of restoring power to the consoles with our own resources, I was shown around the city, but we soon discovered that the city's shield, which had protected it from the water for so many years, was starting to collapse as the city ran out of power, and we didn't have the resources to power it up on our own-"

"Hold on; we're only protected as long as the city has power?" John said, looking anxiously at her.

"It's only an issue if there are too many people in the city," Elizabeth interjected. "Given the date you just gave me, the city has enough power to exist in this state for another two decades before its power runs out completely if nobody else came here, and with only two of us inhabiting it we have enough time to consider alternatives."

"Which are?" John asked.

"Let me finish, and I'll answer those questions," Elizabeth said, smiling briefly at him before she continued. "With most of the search teams drowning before we could get them back to safety, and unable to leave the city via the Stargate due to our power shortage, Doctor McKay tried to see if he could activate the Stargate while I retreated to an area above the control room, where some of the team had discovered… well, the best analogy would be 'space shuttles'."

"Shuttles?" John repeated, his shock pushed aside by that particularly interesting news; the time travel thing had been cool and shocking at the same time, but at least the news of space shuttles was just cool. "There are spaceships here?"

"They're small, but they can operate in space, yes," Elizabeth said. "As the city continued to drown, a few of us tried to escape in one of the ships after the control room flooded and there was no other choice- everyone else was trapped in other parts of the city by watertight bulkheads-, but it… well, it seemed to be slightly different from the others when we first used it, but we weren't expecting it to send us back in time when we tried to escape."

"Really?" John said, increasingly interested in this story. "How far back did you go?"

"Around ten thousand years," Elizabeth replied, her expression becoming more solemn as she continued to talk. "Back to when Atlantis was originally inhabited by the Ancients… and back when they were at war with the Wraith."

"The Wraith?" John repeated, the name inspiring a sense of fear in him even without the harsh edge that had appeared in Elizabeth's tone when she spoke the name. "I take it they're bad guys?"

"They drain the life force from humans in order to survive themselves, aging them to death in a few minutes," Elizabeth said grimly. "I'd call that 'bad', wouldn't you?"

"Yeah," John said, nodding in agreement before he looked at Elizabeth. "So… what happened?"

"Well, we learned later that my pilot- who had the ability to control Ancient technology due to a unique gene sequence we'd discovered back to Earth- had managed to activate a temporal drive that had been included in the ship we were using," Elizabeth explained. "I was rescued from the crash, but the people I was in the ship with at the time… well, they didn't survive the impact."

"Oh," John said, uncertain what else could be said after hearing that kind of story; the deaths were tragic, but considering that her entire expedition had died in the story she'd told him, a few more deaths didn't seem to matter that much. "So… what happened then?"

"When I woke up, I was met by an Ancient who introduced himself as Janus, the inventor of the time machine, I'd just used," Elizabeth explained. "He brought me before the Atlantis High Council to explain my situation, and they told me about the Wraith and how they had submerged the city to protect it from their continued assault. A recent attempt at negotiating a truce had failed; one-on-one, the technology of Atlantis was more than a match for any Wraith ship, but the Wraiths' numerical superiority outweighed that advantage significantly. With defeat only a matter of time, they intended to return to Earth through the Stargate after recalling all offworld forces."

"Makes sense," John said. "So… what did you do?"

"Well," Elizabeth explained, "my first step was to ask if I could use the time machine to return to my own time with a fully-charged ZPM, but when Moros- the High Councillor- refused because of the potential dangers of tampering with time, and the rest of the Council simply agreed with his decision and only conceded to amend their plans to prevent anyone coming back to this city at all, Janus and I had to come up with an alternative plan to save my team and Atlantis."

"Which was?" John asked.

"After Janus worked out how much power would be needed for the shield to remain functional until my team would arrive here in the future, he determined that it might be possible to keep the shield functioning by alternating the remaining Zero Point Modules; that's the name for the power source the city uses," Elizabeth explained. "Instead of having all three of them working together constantly for the ten thousand years needed, each one would supply power to the city for a third of that time… so long as somebody remained behind to rotate the modules sequentially from one to the other."

"And that was you?" John asked.

"Using the stasis chambers to freeze me until the time came to exchange one module for the next," Elizabeth confirmed, looking down at herself with a grim smile. "It wasn't a perfect solution, of course- even Ancient technology couldn't completely stop me aging during such a prolonged period, just slow everything down to the point where I would still be alive now-, but Janus was able to program the system to revive me twice at intervals of approximately three point three thousand years so that I could rotate the ZPMs, instructing me on how to reactivate the process and inputting commands to commence final revival once my team arrived… or you, in this case."

"Me?" John said, looking at her in confusion.

"The city activates when it senses the presence of a living being in it," Elizabeth explained, indicating the illuminated corridor around them. "Your presence must have prompted the city to activate my stasis chamber and release me."

"So… I woke you up early?" John said, looking apologetically at her, the implications of the time difference she'd mentioned earlier hitting him. "I'm sorry…"

"Don't be," Elizabeth said, smiling reassuringly at him.

"But… I mean, you gave up your entire life for your expedition, and now you'll never see them again..." John said, his mind flashing back to the people he had left behind on Earth before he pushed that aside; his friends were more casual acquaintances at best, and he couldn't honestly say that he was going to miss his family after that last argument between him and his father…

"No," Elizabeth said, smiling reassuringly at him. "I gave up a life; my younger self is still out there, and she has the best part of her life waiting for her when she gets here, with the potential to spend years exploring this galaxy and leading the expedition…"

She looked thoughtfully at him for a moment, a contemplative expression on her face, before she came to a decision and smiled at him. "And… you'll be here to help her?"

"Me?" John said, looking at her in surprise.

"You've made it this far without breaking down in a panic, and from what you've told me, you have a particularly strong version of the gene allowing you to control er technology, if you were able to activate the teleporter that sent you here just by touching it," Elizabeth explained, smiling slightly at him. "You've got the potential to really make a difference here, John; if you want to stay here-"

"I actually can't leave," John pointed out. "The… teleporter… that sent me here… I think it broke down."

"Oh," Elizabeth said, nodding in understanding.

"But… what about the Stargate you mentioned?" John said. "Couldn't we-?"

"If we go back to Earth at this time, there's no way of knowing what could happen," Elizabeth said, her expression grim yet apologetic as she looked at him. "So many of the threats that the SGC have defeated once they went into operation were only possible because of the scientific knowledge we had gathered over the years; if we make them aware of what the Stargate is capable of too soon, they may start travelling through the 'gate before civilisation is equipped to cope with what they'll find at the other end…"

"Oh," John said. "So… you mean… if we go home… we could put Earth in danger?"

"Or the government may decide not to use the Stargate at all and the rest of the galaxy will continue to suffer because of the enemies we defeated and are no longer there to stop," Elizabeth said, looking apologetically at him. "I don't know what we can do out here, but if we just wait here, we have a chance; the expedition will be here in… well…"

"Over two decades," John said, his expression becoming grimmer as he took in what he'd just learned; no matter what else happened, unless he wanted to risk putting the entire planet in jeopardy, he wasn't going to go home any time soon…

"John?" Elizabeth asked, her words bringing him back to the present.

"Sorry; lost in my memories, you know how it is," John said, shaking his head as he looked back at her. "Long story short, from what she- you- whatever you want to think of her as- told me, her arrival in Atlantis had resulted in the city's last few power reserves being depleted after they'd been keeping the shield active for so long, resulting in the shield collapsing and the city flooding as the expedition's presence forced it to reactivate old life support systems."

"Oh," Elizabeth said, lost for anything else she could say in the face of such a statement; what was the appropriate reaction to make when hearing about the life you would have lived before your own actions changed history? "How did you meet her?"

"She'd been automatically woken up from stasis when the city detected someone else in it, the computers were able to direct her to where I was running around, and she went on to tell me all about what had happened to her once we'd introduced ourselves," John explained. "After I'd been filled in on her personal background and the basic details about the history of the Ancients and Stargate Command, she spent the next few days telling me everything she could about the Ancients, Atlantis, the war against the Wraith, the technology I could control in the city, a crash course in the Ancient language, how to use the Ancient database…"

"She taught you all that?" Elizabeth asked in surprise (Right now it was easier to think of this woman as someone else rather than another version of herself; it just became too complicated when she thought about the temporal ramifications of the situation in depth). "In… what, a few days?"

"She'd learned a fair amount of what she taught me from the Ancients when she'd arrived in the past; considering that she knew what to expect from me regarding my pre-existing knowledge without the cultural gap that she'd had to deal with during her lessons, it was actually rather simple," John explained with a casual shrug. "Once I had the essentials down, she was able to hang around for a few days to help me get a good grasp of everything, and then she accompanied me to a particular old outpost where I was able to recover a spare Zero Point Module to restore the city's power; the one that was left didn't have much energy left to do anything more than power the shield for a few more years, and that was only going to work if I was doing nothing more than staying in the city all that time."

"Which you couldn't do if you wanted food, right?" Elizabeth said, nodding in understanding.

"Right," John confirmed. "I was able to find a couple of abandoned planets with some crops and cattle yards that I could use- even managed to find my weapons at an old crash-site, even if I wasn't able to access the ship's databanks to learn where it came from-, but I started growing my own food in a few botany labs over here that you haven't found yet; I've taken a few things from your supply lockers since you arrived, but otherwise I've been pretty self-sufficient here."

"When did you start fighting the Wraith?" Elizabeth asked.

"Once I'd sorted out my food situation, dealing with everything else just… fell into place, really," John said. "I spent some time scoping out old Wraith bases in cloaked ships to see what I could see, intercepted a few Culls, even managed to destroy a few ships once I'd worked out where their weak spots were…"

"And… when did you start wearing the mask?" Elizabeth asked.

"After my first trip to an inhabited planet," John replied. "I managed to drive off a Wraith scout team, but then they saw my face and…"

"And they reacted like Ronon and Teyla," Elizabeth finished for him, looking sympathetically at him before her natural curiosity reasserted itself. "What does-?"

"They thought I was a Wraithspawn," John said, "Basically, Wraithspawn are what happens when Wraith feed on pregnant women; the kids develop birth defects due to the Wraith hormone in their systems, they develop various personality defects… they don't have a great reputation, as you can guess."

"So… you started wearing a mask and cloak?" Elizabeth said, looking at him in surprise.

"I was a teenager when I got here; naturally I liked superheroes," John said, smiling at her. "I mean, it took a while to make the mask, and I've spent some time upgrading it since- it was just a bit of metal when I started wearing it-, but-"

"No, I mean… why did you do that?" Elizabeth asked, looking at him in confusion. "If they… well, if they reacted like that…"

"Why did I bother saving them?" John said, smiling slightly at her. "Being treated like that sucked, don't get me wrong, but I wasn't going to let people die just because they freaked out when they saw a face that looked like it was hit by the metaphorical ugly stick.

"She asked me to do what I could against the Wraith to protect the innocents of the Pegasus Galaxy from them, as well as keeping Atlantis safe, until you were able to return here; considering everything you'd done for them for around ten millennia, coupled with the fact that we didn't know what the consequences would be of going back to Earth now, it seemed kind of petty to object to that kind of request when I didn't have any real reason to want to go home anyway."

"Uh… consequences of going back to Earth?" Elizabeth asked.

"You were worried about what might happen if we learned about what the Stargate could do before Earth had developed all of the scientific advances it had used in the timeline you knew; it was easier to just stay here and let everything back home unfold as it should," John explained, before he continued his story. "I spent some time gathering up any spare ZPMs I could find, keeping them in storage in an old asteroid belt I found- it might have been a planet at one point, but I don't know what happened to it and it didn't seem worth trying to find out- just in case anything went wrong; I didn't want to run the risk of using too many of them too quickly unless I had to, particularly when one was all I needed to keep the city running. Having identified the one with the least amount of power in it, I plugged that into the city and used it until you came here; add in the time I've spent going back and forth, stopping Culls and taking out Hive-ships, and… well, you've got the basics of my history from the stories already."

"I… I see," Elizabeth said, taking a moment to process everything she'd just heard before she looked uncertainly at John. "And you did… all this… because I asked you to?"

"You asked me to do what I could because you believed that I could make a difference," John said with a shrug, as though that was all that needed to be said about the situation he'd been in for so many years. "It was risky, but I had to give it a shot; I didn't want to let you down."

"And… that was it?" Elizabeth said in surprise. "You'd only just met me, and I… well, I died a few days after that…"

"You believed in me," John repeated, in a manner that made it clear that her belief in him had been all that he really needed…

No, Elizabeth thought to herself, pushing the immediate thoughts inspired by that comment aside.

She might be around his age now, but considering that he'd met the old woman in the stasis container beside them when he was a teenager, she couldn't be anything more than a mentor figure to him. She was his… the Gandalf to his Frodo, or the Obi-Wan to his Luke (And why weren't there any decent female mentor roles that she could compare herself to off the top of her head); that was all there was to it.

She ignored the little part of herself that was remembering how she'd always thought about something more even before she'd learned that John came from Earth; he'd been inspired by her other self, and that was the reason for his interest in keeping her safe.

"So…" she said, looking at him with a slight smile as she prepared to tackle the central issue facing them, "now that you've told me how you came here, shall we… tell it to everyone else?"

For a moment, John simply stared at her in silence, a slightly panicked expression on his face, but he calmed down after a few moments, smiling briefly at her.

"I've been in hiding long enough," he said. "Time I met everyone here face-to-face."

It was a simple statement, but after almost three years of seeing him operate in secrecy, the knowledge that he was going to end that time because she'd asked him to meant more to Elizabeth than she thought she could ever hope to express.

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