Title: Beginning's End (Complete)
Rating: NC-17 (PG-13 version also available in a link below.)
Categories: Sheppard/Weir, AU, romance, Action/Adventure, Angst
Summary: During "Before I Sleep," the alternative version of John Sheppard lived as well.
Beta'd: This story was beta'd by the fabulous shayz, who gave me constructive criticism and reworked entire passages for me to make them more coherent. I think I have a better grasp of the English language now, all because of you, and this story, I think, would have turned out vastly different if it hadn't been for your fabulous additions. I don't lie when I say your relentless work made this story more than a thousand times better. :P
Warnings: Character death (it is based on "BIS") Language, violence, and sexual situations.
Spoilers Main spoilers for "Before I Sleep", "Rising", and "Aurora". Nominated for
Best Sheppard/Weir Drama FicIn 2007 Stargate Fan Awards

. . . And then there were two.

Staring up at the unfamiliar ceiling of the Atlantis Infirmary, John Sheppard debated on the merits of whether his life had turned into a science fiction movie or a horror movie.

He decided it was fifty-fifty. The time traveling and the aliens and the galaxy far, far away made him think of Star Wars and Star Trek and all the other Star-related (huh, Stargate. Well, wasn't that just convenient?) things he'd seen in his life, but the death and chaos that had followed him since he'd first stepped through the wormhole and onto Atlantis made him rethink things through. Horror was definitely a part of his life now.

Ten thousands years into the past and a galaxy away from home meant only one thing: everybody he knew was dead. Or not yet born. He wasn't really sure if there was much of a difference, especially since the end result was the same. Considering he'd just woken up from a nightmare of men and women screaming and drowning under an avalanche of water . . . which had actually happened; well, it made the whole 'dead theory' seem more concrete than any abstract concept of time-travel.

Freakin' time-travel, John thought, scrubbing both hands over his face. The drugs in his system were good at dulling physical pain – or so Janus informed him – but they also made him incredibly restless when he wasn't sleeping. He had an inkling it also made him slightly loopy. All things considered, there was no way he should have been able to take what had happened to him as lightly as he was right now.

There should have been yelling and cursing and not a small bit of violence involved on his part, but John only considered himself on the border of irritation and restlessness. It had to be because of the drugs.

In any case, his mind refused to be a good boy and shut down, and the frustration level seemed to build the longer John stayed awake. Hooked up to the high-resolution holographic monitors and an IV drip that contained an unfamiliar reddish substance, John never hated the idea of being sick more. He didn't feel sick, though, not beyond a slight case of fatigue and dizziness every time he tried any bold movements (like standing up too quickly; that had been a bad idea), but the list of injuries Janus had told him he sustained in the crash ran longer than the offenses at his almost-court-martial.

He should be dead. They should be dead.

With the number of injuries inflicted after their ship thingy got blown out of space and into a freezing alien ocean, under normal medical care, they would be. But they were in Atlantis now, under the care of the Ancients, and there was nothing normal about that.

He glanced over at the infirmary bed to his right. Dr. Elizabeth Weir, his sole companion, lay turned to one side with her back to him. He didn't think she was sleeping, but didn't test his theory either. He covertly scrutinized her – noticing that her body under the thin white sheet that made her look incredibly small and vulnerable – and with the knowledge that she was the last thing familiar to him, he wondered what he should call her. Dr. Weir seemed so formal… considering.

He'd known her all of seven days, and although he knew she was a diplomat of some kind (an internationally acclaimed negotiator if he heard right), she was as much a mystery to him as anything else at the moment. He knew she was well-respected, enthusiastic, clearly a little bit innocent – it shined through every time she'd spoken of Atlantis – but she had a deep sense of duty that John respected.

Other than that, however, he didn't know anything about her: where she came from, what she left behind, what she had expected from the expedition or from him. But when she approached him about joining the expedition, she'd been so eager, so animated.

Now, though, she simply looked ashen and worn out and not entirely because of the drugs she was similarly hooked up to. He should say something to her; something comforting and wise, but words failed to mean much under the weight of the realization that they were, literally, the last two of their kind.

A hundred cheesy pick-up lines filtered through his mind. It was like something out of a bad '80's movie, he decided definitively. They were the last man and woman from Earth, fighting for their survival in an unknown galaxy. Of all the B-grade plots to be placed in, John would much rather preferred to have been stranded on a deserted island instead. At least there, he wouldn't have had to consciously ignore the fact that every man, woman, and child he'd ever met was dead!

Suddenly and overwhelmingly irritated, he sat up and viciously pounded his pillow with the ruse of getting a more comfortable shape out of it; though really, he just needed to punch something. The action was audible and distracting enough that Elizabeth noticed, even with her back to him, and turned over.

"It's all so fucking morbid," he muttered, without meaning to.

Her lips curled upwards, ruefully. "Yeah, it really is."

Her green eyes were dull, empty in comparison to the outright wonder he'd seen reflected there only twenty-four hours ago. It ratcheted up the frustrating level another notch and John had to fight the urge to rip out the IV and jump off his bed, knowing that the action would only result in him ending up in a pathetic lump on the floor.

"How much longer are they going to keep us here?"

"Here in Atlantis?" Elizabeth asked, raising an eyebrow. "Or here in the infirmary?"

"Both," John groaned. "Either one. I don't care."

She licked her lips. "Janus said we'd have to stay here overnight, but tomorrow they'll move us into other quarters. He doesn't think the dizziness and fatigue is going to last much longer."

John nodded, unable to take his eyes away from her. At least she was real.

She sighed, shifting in her bed again, and stared up at the ceiling. Her voice turned into such a soft whisper that John had to strain to hear it. "I keep thinking about Rodney and Dr. Zelenka. Colonel Sumner. The thirty-eight other people that walked through the Stargate under my command and then…" She shook her head, fighting back strong emotions. "It shouldn't have ended that way." She slowly sat up and turned to him, determination settling into her eyes. "And I've been thinking, it's not going to."

John raised an eyebrow. "Okaaay. Are we going through the denial stage of the evening? Because if you give me a few minutes, I could probably join in on the fun."

She arched an eyebrow. "I'm serious, Major. We traveled in time," she said, voice level. "And we can travel back… or forward, as the case may be. Point is, we can prevent any of this from ever happening. All we need is that ship we came in."

"The one that we crashed into the bottom of the ocean and is now in little bits and pieces?"

Elizabeth's enthusiasm sagged with her shoulders. "Okay, I admit, that's a set-back. But they probably have another time-travel machine of some sort. We just have to convince these Ancients to allow us to use it."

John had to admit, he was beginning to see the beauty of this idea. It could work. And hell, if it had even the remotest chance of working, then he would make damn-well-sure it did work. Whether it wanted to or not.

"Janus seems like a decent man," Elizabeth continued. "If we talk to him… explain. He'll agree."

"If not," John added, trying to keep the edge off his voice. "I'll convince him otherwise."

Elizabeth gave him a warning look. "Careful, Major. These are the Ancients we're talking about. You can't bully them. And getting on their bad side is not something I want to do. We have to be very careful about presenting the best image possible. For this to work, they need to want to help us."

John raised surrendering hands and nodded once. "You're the boss."

She immediately swallowed hard and turned away, like there was a bitter aftertaste in that statement. She laid back down, staring up at the Atlantis ceiling that John knew offered nothing but a smooth flawless texture to scrutinize. For a moment, he wondered what dark thoughts circled inside her head. The images and screams. If they were the same as his. He had a gut feeling that Elizabeth was struggling to keep her head clear, just like he was.

"Hey," he said, surprised by the encouraging tone in his own voice. "We'll fix this. We'll get out of here and save them."

"We have to," Elizabeth said softly, but firmly. "Otherwise I don't know what the hell I'll do with myself."

Hours passed as they remained confined to the infirmary under the mandated observation and rest routine. A few of the Ancients that filtered through the place seemed far more interested in other business than observing them. John found that a little unusual considering Elizabeth and he represented two honest-to-goodness time-travelers from the future. But apparently it took more than that for anyone on Atlantis to get excited. Mostly, they flit around the area with a forcefulness and concentration that exhausted John just by looking at them, all tense and jittery.

Something was up.

He asked, but no one answered. He couldn't even charm one of the "nurses" into telling him what all the hubbub was about. She simply blinked at him, but before John could explain the term, she told him to rest and turned her back on him.

As the nurse scurried away, John's gaze collided with Elizabeth's. "They're obviously not allowed to tell us anything, Major." She managed to look both amused and pitying at the same time. "There's no use trying."

"Yeah, well, there's only so much rest I can take," he muttered, getting anxious. "Shouldn't we be doing something? Or they be doing something? We've traveled from the future and they've barely given us a 'how-do-ya-do' before shipping us off to a corner. They've gotta be curious about us."

"I was actually thinking the same thing. I know if I were in their position, I'd want answers as soon as possible."

John studied the room. The constant ebb and flow of activity as people went in and out was… wrong. "I think they've got something more pressing on their minds."

An anxious look flashed over Elizabeth face; that idea didn't sit well with her. John wholeheartedly agreed. He hated being in the dark, almost as much as he hated being useless. The idea that the Ancients were in the middle of something that put Elizabeth's and his situation on the back burner didn't bode well for them. They needed the Ancient's undivided attention and help.

Otherwise, they were just plain screwed.

Sometime later, they were finally released from the infirmary, and although his legs initially seemed unstable and weak, John refused to be pushed in a wheelchair and stubbornly willed his body upright as they were escorted through the hallways. Elizabeth, having been in better medical shape from the beginning, didn't struggle as much as he did, but John was pretty sure the healthy color in her cheeks had more to do with their change in environment than anything else.

Unlike the white sanitized infirmary, the rest of Atlantis seemed to be constructed for beauty. John had never been one to notice much of aesthetics or architecture, but the beauty of Atlantis was something that anyone who stepped foot on it would automatically notice. The entire City was all smooth surfaces and sleek sophistication. Having spent the majority of his life in one bland military facility or another, it was a nice change to see vibrant colors, wide open spaces and elegance in structure that was visually pleasing.

Elizabeth eyed the surroundings with barely concealed wonder, and that dull emptiness left her eyes in an instant and, if only for a moment, it seemed as if she'd forgotten the events that brought them there.

They were led into a conference room where a semi-circular table in the center held three people on the outer rim, like judges in a panel. Apparently, this was the Council that Janus had mentioned Elizabeth and John were to meet. Remembering Elizabeth's earlier words to be on his best behavior, John pasted on a casual, friendly smile. These people held his life and those of his people in their hands and he wasn't about to piss them off. He nodded at each as they made their introductions, and then Elizabeth introduced herself and John.

Melia, a slight woman with long black hair and what looked like Asian eyes, seemed to specialize in the same brand of congeniality as Elizabeth. They exchanged pleasantries, and while Elizabeth informed her of their current health and well being, John eyed the oldest Ancient in the room, Moros. He sat next to Janus and stared at John with an expression that reminded him of the contemptuous looks Principal Hading use to give him in elementary school.

John smiled in return, trying for innocence, but this simply succeeded in turning Moros' expression more sour. John cleared his throat as a few more people filed into the room. As the last of the introductions were made, Moros called the meeting to order.

Melia officially greeted them, "We welcome you to the city of Atlantis."

"Thank you," Elizabeth nodded. "Major Sheppard and I are both honored to be here."

Melia's smile faltered. "Unfortunately, your arrival has come at a time of great conflict. We've been under siege for many years and have submerged our city as a measure of protection."

"Yeah, we know," John replied. "It's how we found the city when we first came through the Stargate."

Moros cast John a suspicious look. "From Earth?"

Elizabeth nodded, but it was Janus that answered for them. "Ten thousand years from now." He smiled eagerly, reminding John for a moment of some of the zealous scientists on the expedition. The ones he hadn't gotten the chance to know. "It should be duly noted that our actions have succeeded in protecting the city for so many years."

Melia interrupted, dispensing with the pleasantries. "Let us hope their arrival has not altered this eventuality. By directly encountering the Wraith, they may have already set in motion a chain of events that could lead to a future far different from the one they left."

John paused, and then raised a hand in the air. "Uh, sorry. What's a Wraith?"

Several people stared at him with wide eyes and then shifted in their seats uncomfortably. John felt layers of tension settling into the atmosphere like a heavy, damp blanket and his stomach clenched in response. After a moment, Moros answered, "The Wraith are a species of this galaxy that we have been at war with for the last hundred years. They have a formidable army and use a level of technology that rivals our own."

Janus sighed, but it sounded more like a groan to John. "They also suck the life from us by feeding off our bodies, and have vowed to eradicate our existence from this galaxy. Let us not mince words, Moros. We are at war." He turned to Elizabeth and John with haunted eyes, and stated emphatically, "And we are losing."

John appreciated the man's bluntness, but even as he marked another tally for the reasons to like the guy, he felt a sickening chill work up his spine. If the Ancients were losing, he couldn't imagine the threat these Wraith truly posed. Even worse was that no one bothered to counter Janus or alleviate some of the bleakness in his words.

Melia cleared her throat, looking down. "There is one last attempt to negotiate with the Wraith. We are sending a delegation protected by our most powerful warships in the faint hope of negotiating a truce. They will be leaving in two days from Atlantis."

"It is a fool's mission," Janus replied, forcefully. "You cannot reason with the Wraith."

"If that plan should fail," Moros replied, "then we must await the last of our off-world transport ships to return before beginning the evacuation through the Stargate."

"Abandon Atlantis?" John heard the shock in his own voice. He knew it was going to happen but he never expected to be there at the precise moment it occurred.

Elizabeth shared John's surprise. "Where will you go?"

"We are returning to Earth," Melia informed. "You are welcome to join us, of course."

Elizabeth smiled a tad forcefully. "Thank you. That's very kind, but I'm sure you understand our desire to return to the future – to our people. We were hoping we would be able to use a time machine again, and program it to arrive at the precise moment we came through the Stargate – and if it was possible, and you had a spare ZPM we could take that back with us as well. That would help us considerably. See, the power systems of the city were virtually depleted–"

"No!" Agitated, Moros shot up from his chair. "Enough of this tampering with time. Causality is not to be treated so lightly."

Janus looked pleading. "No one is treating it lightly."

"You are!" Moros glared at him. "With your insistence on continuing with these experiments despite the condemnation of this Council. We ordered you to cease these activities and yet here we sit, face-to-face with visitors from the future who arrived here in the very machine you agreed not to construct."

Janus didn't back down. "We are about to evacuate this city in the hope that it will lie safe for many years and then, one day, our kind will return." He looked pointedly towards both Elizabeth and John with gratitude. "And they have. It is because of my experiments that we now have the opportunity–"

"Enough!" Moros interrupted. "We have no time for this."

"Well," John said, catching onto Janus's frustration, "with all due respect, make time."

"John," Elizabeth warned.

Ignoring her, he faced Moros. "We're not meant to be here. I understand you've got bigger fish to fry at the moment, but you can't shuffle us off into the corner and then forget about us."

"No one is suggesting we do that," Melia countered.

"No? Then what are you suggesting?" John asked in a demanding tone. "Dr. Weir and I are not from here. We deserve to go back to our time and save our people."

Moros looked angry enough to spit nails. "You do not even realize what you are talking about! Janus, explain to our guests the concept of time-travel that is obviously gone beyond their comprehension. Explain to them why they can never change their past."

Elizabeth stood at this point, confusion evident as she turned to Janus. "What is he talking about?"

Janus frowned. "Time-travel is . . . a very complex system of parallel universes. The moment you traveled to our time, you created a separate reality – universe – which is divergent from your original one. What has happened in your original reality is no longer within our abilities to control or change. Should you choose to travel in time again, forward from here, you would in fact be traveling to another parallel universe based on this past, this time. You could, theoretically, save them, but they would not be your people. And, more than likely, you would encounter your own doubles, which would lead to the unpleasant side-effects of phase shifting and–"

"So you're saying," John cut in, "that our people are dead, and there's no changing that?"

Janus nodded solemnly.

Elizabeth looked pale enough to faint for a moment, but she swallowed hard and forcefully recovered. "Still, we can save others. Save our doubles and their people. We can't let the same disaster happen twice."

"No," Moros replied, firmly. "Time is not to be meddled with so lightly. What will happen must happen. It is not for us to decide fate."

"What do you suggest we do?" John asked, outraged. "Just sit back and let–"

"You have no choice in the matter," Moros interrupted. "I am hereby ordering the destruction of any time-traveling device, and all the materials connected with its design. You are both welcome to return to Earth with our people." He paused, standing tall and rigid. "You shall not be returning to yours."

John turned incredulous enough to see red in every direction, and despite trying to get in another word edgewise, Moros effectively ignored any further protests and walked out the door. Both Janus and Melia stayed behind, trading conspicuously less-than-pleased glances with each other over the outcome of the meeting. Had John not been fighting the urge to chase down Moros and convince him to change his mind, he might have taken advantage of the moment.

Luckily, Elizabeth did. She quickly crossed the room and quietly conversed with Janus, before both of them turned to face Melia as a unified front. John had enough time to cross the room to hear small snippets of the conversation.

"You need to talk to Moros," Janus implored. "Dr. Weir and Major Sheppard were brought here through no fault of their own. They shouldn't be punished for it."

Melia regarded them with sympathetic eyes. "They are free to come back with us to Earth and live among our kind–"

"They need to return to their time, not remain in ours."

"That is not possible." Melia bowed her head slightly. "I'm sorry."

"Sorry doesn't get us anywhere," John said, coming up behind Elizabeth. "We need some damn help."

Elizabeth sent a quelling look in his direction, and seeing as his other outbursts hadn't done any good, he subsided. She turned back to Melia. "I don't think you understand how far we've come, or how much our people have sacrificed in the hopes of meeting you." She paused and John saw the glimmer of innocence in her eyes that he'd first seen in Antarctica. "We call you the Ancients. The Gate builders. We've crossed galaxies in the hopes of finding a great people. Please, is there no other way you can help?"

John understood now why Dr. Elizabeth Weir was internationally acclaimed diplomat. And for a moment, it seemed like her words were having the necessary effect on Melia. "We could block the Stargate permanently after the evacuation. That way, in the future, your team will be unable to come here."

Janus immediately looked incredulous. "If they can't come, the city may never be found."

"But the lives of their expedition will be saved."

It surprised John that Elizabeth didn't even bat an eyelash at the suggestion. "Thank you for your generous offer but we are explorers - just like you."

Before John could cut in to buffer Elizabeth's words, Janus spoke up again. "Which should come as no surprise since they are the second evolution of our kind. Major Sheppard even shares some of our genetics. Don't you understand? This city will survive ten thousand years."

Words stalled on John's lips as Melia struggled internally, but eventually she turned back to the group with resolute eyes. "I'm sorry," she said again. "The Council's decision is final." She turned and walked away, leaving Janus and Elizabeth speechless in her wake.

John felt like the last person in this place with any bit of sense whatsoever.

He didn't say anything at first, though. He waited impatiently as Janus gathered up his things and escorted them back to the Infirmary for their over-night observation, giving half-hearted words of comfort to them along the entire way. John did his best to contain his anger, well aware that Janus looked to be the best ally they had in this place, but as soon as Janus had cleared away to return to his laboratory, John turned on Elizabeth and decided to let loose.

"Are you completely insane?"

She stopped walking towards her bed and arched an eyebrow at him. "Excuse me?"

He exhaled hard, reined in his anger and started again. "Why didn't you agree to have the Gate closed off? It would save the expedition."

Her mouth gaped open in astonishment as she turned to face him fully. "And prevent anyone from ever discovering Atlantis again."

He couldn't wrap his mind around her logic. "What good would that do if less than twenty-four hours later they're drowning at the bottom of the ocean floor? They're going to die."

"Not if we do something about it first."

John stared at her in utter confusion. "Were you at the same meeting I was just at? Because I don't think you were paying attention to the definitive decision that happened in there to screw us over!"

"Major!" Elizabeth exclaimed, voice turning ice-cold. "I understand your disappointment, but now is not the time to lose our composure."

"It's not the time to lose touch with reality either. How are we possibly going to save them?"

Elizabeth opened her mouth, only to falter. "I-I don't know... but there has to be a way."

He ran a hand through his hair, and although a part of him understood her need to think there was still hope to change the past - future - whatever! - John had always been raised in practicality.

And in practical terms, they were fucked.

The Ancients weren't going to help them, not under Moros' command. And without the Ancients' help, they had no avenues of possibilities. They had to face reality. If given no other option, John didn't want to shut the door on the one choice they did have available. Closing off the gate to any future expeditions would save lives, and above all else – even above Elizabeth's optimism – he had to make sure that those future lives were saved.

"There might not be a way," he said, breaking the silence. "If they don't allow us to use the ship, then we have to close off the gate." The very idea seemed to repulse every fiber of Elizabeth's being, but he could see the seeds of hesitation sprouting. "This is what you hired me for," John reminded her. "To give you military options. Provide you with cold hard facts. And the reality of the situation is, Doctor, as of now, any future expeditions are headed towards the same fate we just escaped from. We can't afford to let the vain hope of exploration blind us from that."

"All this knowledge," she said, waving her hands around in futility. "This entire place… it'll just lay to waste at the bottom of the ocean."

"With all due respect to this place," John said coolly, "better it than our people."

A nurse came up before Elizabeth could respond, and instructed them – or ordered them, more like - back to bed. John cast Elizabeth one long, hard look but she climbed into bed without even glancing back at him. He couldn't blame her for suddenly turning defensive. He wanted to convince her – and paradoxically, a small part of him also wanted to believe in her too – but he couldn't imagine any way and he was a pretty imaginative guy, always thinking outside the box. But this box had sealed them in. Her optimism was refreshing, but unwarranted. The more he thought about it, the more he realized the complete bleakness of their situation.

Elizabeth turned her back to him again, but he could tell from her rigid shoulders that sleep wouldn't come easily for her tonight. Right now, he was glad they had never worked within the same command structure. He couldn't imagine they would have seen eye-to-eye on much. He respected her, but he didn't understand her. They were complete and utter opposites, and that boded disastrous for any decisions that had to be made bilaterally.

He spent the night tossing and turning, hooked up once again to a red substance that should have lulled him to sleep but didn't. There was too much on his mind. Try as he might, he couldn't shut his brain down. The often heard rustling of Elizabeth provided John with a few distractions, if only to break the awkward silence. He knew she didn't want to admit defeat - neither did John, because he had the feeling that the images of people he barely knew, yet still felt responsible for, would never stop haunting him otherwise.

He remembered Dr. Rodney McKay, trapped in the Gateroom as millions of gallons of water poured in. He thought of Lt. Ford, fresh out of military school and as green as he'd ever seen them come; Dr. Zelenka, with the thick Czech accent that sometimes made him difficult to understand; The Scottish Dr. Beckett, who had nearly killed him with the squid-like drone and then profusely apologized about it afterwards. Sgt. Bates, Peter Grodin, and the other two dozen men and women he barely knew and never had the chance to get to know also flashed across his mind.

He thought about Colonel Sumner last. The commander's opinion of John had not been flattering. Looking back, John realized that Sumner recognized him for what he was, and knew his place was not with the expedition. Right now, he would give anything to be able to tell Sumner that he was right after all. This wasn't his place, and he was not a man capable of handling the fallout of the biggest mission disaster in the history of mankind.

Everybody had been right about him. Everybody except Dr. Elizabeth Weir, who saw something in him that was obviously never there. He had wanted to believe he still had a chance left. He had wanted to revive his flailing career and prove to all those military bigwigs that he wasn't a complete loser destined for low-level posts.

Lying there in the infirmary as the last of two survivors of the freakin' second evolution of humanity, John never felt the sting of his inferiority more in his entire life. He glanced over at Elizabeth, and felt resentment build up. He had no right to feel that way, and he knew she didn't deserve it, but the fact remained: Dr. Elizabeth Weir was the only reason he was in this mess.

He turned over on his side, his back to hers, and wondered why fate had ever interceded to bring this woman into his life.