Definite spoilers for 'Allies' in this chapter. Italicized dialogue is taken directly from the episode
Later Troy sat on his bed in his darkened quarters attempting to meditate the way Teyla had taught him when he'd been a child. He could hear the faint hum, the almost whisper of Atlantis in the back of his mind. When he'd been a kid growing up in the city he'd never really been consciously aware of the connection he'd had with the city; the energy, the almost whisper, the way Atlantis was alive in it's own way - not quiet sentient, but more than just an inanimate object.
He remembered how after Atlantis had been destroyed, he'd felt like a part of him had been viciously ripped out, leaving a gaping hole in his being. But here in this place in this time, that hole had been filled, he was whole again. Yet at the same time he felt lost and alone, like he literally had the weight of the world on his shoulders.
With a sigh as heavy as a stone Troy gave up on trying to meditate and began to pace. He had a huge decision to make that would have long lasting and far reaching consequences and a very small window of time in which to make it. He had been debating with himself for days over whether or not he should interfere with the timeline or just leave it alone. The same thought kept running through his head; Jamas had been right about this being a chance to stop the Wraith getting to earth.
Stopping to look out his window at the ocean Troy rested his head against the cool glass and let himself just listen. He could feel the humming rightness of Atlantis inside his head, lulling and promising, smoothing the edges of his worry and anger. Telling him he belonged here; he'd come home again. With a sudden clarity about what he had to do Troy pushed away from the window and went to grab his combat vest off the chair he'd dumped it in.
Sitting back down on the bed he carefully began to pry apart the lining of the vest. Cautiously he pulled out the two items that he would vitally need if he had any hope of pulling off what he was about to do. The first item was a small canister filled with a substance that was one hundred percent lethal to the Wraith, but completely harmless to humans. The substance was a combination of parts from Carson's retrovirus and parts of the Hoffan serum. By the time the substance had been perfected the Wraith had already attacked earth and destroyed most of earth's defense ships leaving the humans with no way of distributing the drug on a large scale, but even so all off world personal carried a canister with them just in case.
If Troy could place the canister in the right place there would be just enough substance to take out an entire Hive ship. That's where the second item came into play; a Sodan cloaking device. With the cloak Troy would be able to move around the Wraith Hive ship undetected, all he had to do was find away to get aboard the ship.
Breaking into the Jumper Bay, Troy made a mental note to remember to thank Radek for teaching him everything he knew about the Jumpers. After boarding one of the Jumpers he used his PDA to hacked into Atlantis' system and open the bay doors without alerting anyone in the control room. Cloaking the Jumper Troy set a course for the hive ship.
Once on board the Hive ship Troy activated the Sodan cloak and silently made his way to the section of the ship that held the life support system. In one of the corridors he came across Ronon, Rodney, and one of the Wraith scientists. Pausing for a moment with his back pressed up against the wall he watched as the Wraith put its hand on Rodney's shoulder. Instantly Ronon grabbed the Wraith and slammed it against the wall, holding a knife to its throat.
"Ronon, are you crazy? Do you wanna get us killed?" Rodney's gazed shifted around nervously.
"You don't touch him." Ronon growled out at the Wraith.
Trusting that Ronon had things under control and wasn't about to let anything happen to Rodney, Troy continued on his way. Reaching the life support system he worked quickly to get the canister positioned inside the system that scrubbed the CO2 from the ship's artificial atmosphere and redistributed it as breathable air to the rest of the ship. After setting the time delay release Troy took care to leave no trace that he'd been there and made his way back to the cloaked jumper in the hanger bay.
"I should be on that hive when we do this." Rodney stated as the Wraith queen left the briefing room to return to her ship.
Watching the queen leave, Elizabeth turned around a look of surprise on her face at Rodney's statement, "Excuse me?"
"Really?" John was just as surprised.
"I know it's uncharacteristically brave, but I've hacked a lot of their systems under the guise of repairing them. I've convinced them that I should be there to supervise their systems if anything goes wrong."
"And they agreed to this?" Elizabeth was sceptical about the Wraith doing something like that with out an ulterior motive.
"Yes. Plus, now we can freely beam stuff on and off their ships ... " Rodney took a small device out of his pocket. "...I've written a program that will immediately beam me out of there the second I activate this emergency transponder." He smiled proudly as John folded his arms doubtfully.
"You're sure you wanna do this?"
"Of course I don't wanna do it! I just ... I think it should be done."
"Ronon goes along." John insisted.
"Wouldn't have it any other way." Rodney wasn't entirely happy with that, but knew it was John being John.
"And I'd like you on the Daedalus." Elizabeth turned to John.
"No place I'd rather be."
"OK, good. Let's get this done. I'm about ready for our house guests to leave." She was about to say more but was cut off by what sounded like gun shots coming from the gate room. Sharing a brief glance with John and Rodney, Elizabeth hurried out of the briefing room to find out what was going on, the two men followed after her. The three reached the small balcony over looking the gate room just in time to see Troy seemingly appear out of nowhere, his P-90 pointed at the Wraith Queen.
Sodan cloak still active, Troy skillfully maneuvered his way through the city from the jumper bay to the gate room. Finding an out of the way place where he could see the briefing room doors, Troy waited for the Wraith to exit said room.
He didn't have to wait long. Once the Wraith were out of the briefing room and had been escorted down the large staircase to the gate room, Troy, using the element of surprise, quickly opened fire on the two Wraith guards. Satisfied that they were down and not getting back up Troy de-cloaked and aimed his P-90 at the Wraith Queen. He ignored the soldiers on guard duty who all had their own weapons aimed at him as well as his parents and Rodney, who he could see out of the corner of his eye, his attention solely on the Wraith in front of him.
"What is the meaning of this?" The Wraith Queen, startled at the sudden appearance of Troy, demanded as she discretely moved to activate the transmitter on her wrist.
"Don't bother." Troy spoke up, knowing what she was trying to do. "As of..." He tilted his wrist to look at his watch, "This moment every Wraith on your ship is dead or will be momentarily. There's no one up there to give away Atlantis. You're all that's left of your crew."
"What do you think you're doing Major?" Elizabeth questioned as she reached the gate room level, John right behind her.
"Stopping the Wraith from learning the location of earth." Troy never took his eyes off the queen, so didn't miss the way her eyes slightly widened in surprise. "Yeah, you heard what I said. I know all about your little plan."
"I don't know what you're talking about." The queen couldn't hide the glare in her eyes.
"Bullshit!" Troy fired a single shot into the Queen's shoulder; painful but non-lethal. This of course caused the soldiers to all tense up even more and tighten their grips on their weapons even tighter, ready to react.
"That's enough." Knowing that he wouldn't hurt her, Elizabeth moved in front of Troy to keep him from trying to shoot the Wraith queen again. After ordering the guards to escort the Queen to a holding cell until she had things sorted out Elizabeth turned her attention back to Troy.
The Wraith Queen wasn't happy in the slightest bit about being locked up and would have protested or even fought back, but she knew she was out numbered. Plus if the young man before her was telling the truth, she really was the only one from her ship still alive, there would have been no point in fighting back. Even if she could have gotten away there would have been nowhere for her to go.
Once the Queen was out of the room Troy handed his gun over to John, knowing the man would be even less likely to listen if he was armed. Without a word Elizabeth turned and headed back to the briefing room, John and one of the guards that had remained ushered Troy after her. In the briefing room John and Elizabeth sat at one end of the table while Troy sat at the other.
"So you gonna tell us what that was all about?" John asked, arms folded and a scowl on his face.
"Should probably get the rest of your senior staff in here first. Save the trouble of having to go over this more than once." Troy leaned back in his chair nonchalantly. At this point he had nothing to hide. He'd just changed history after all, pretty much everything he knew was moot at this point.
Agreeing Elizabeth called Carson and Rodney over the radio and asked them to come to the briefing room. Rodney was there almost instantly, having been hovering around in the control room, Carson took a few more minutes to get there. Once they were all there and settled she turned her attention to Troy. "Now why don't you start from the beginning."
"First, everything I told you about how I got here and all that stuff was true. I didn't come here with the intention of changing history, but I realized that Jamas was right about this being a chance to stop a war, to save billions of lives. His way of going about it may have been wrong, but not the idea. The Wraith never had any intention of forming a legitimate alliance with you. The alliance, their willingness to share information, all of it was nothing more than a ruse to learn the location of earth."
"How?" Elizabeth began to get a sinking feeling in her stomach at how close she'd come to allowing the Wraith access to earth. No matter what anyone said if the Wraith had managed to learn the location of earth it would have been her fault and her fault alone, she was the one who had agreed to Michael's proposal.
"The information they downloaded to you. Within the hive ship's schematics was a worm-like computer virus. Unfortunately the virus wasn't detected until after the Daedalus and the Hive ship, with Rodney and Ronon on board, had already left Atlantis this last time."
"What was this virus designed to do?" Rodney was curious. They'd gone over the Wraith downloads with a fine tooth comb and found nothing.
"It very selectively probed Atlantis' systems without damaging them or exposing itself. Once the hive left Atlantis, the worm began to destroy all of the data they had sent down. It uploaded two pieces of information: one – the Aurora mission reports...and two...the location of every world in your database. Which as I'm sure you all know includes earth."
"Luckily you were able to rescue Rodney and Ronon and destroy the hive ship before it reached earth, but unfortunately not before they were able to transmit earth's location to other nearby ally Wraith ships. Thankfully for us they didn't go after earth right away, they were all to busy fighting each other in their little civil war."
"It was another five years before the Wraith started to show up in any real force in the Milky Way galaxy. Every once in a while during those five years a ship or two might've showed up but it was nothing that couldn't be handled by either earth, the Asgard, the Tok'ra, or the Jaffa. Then something changed, the Wraith stopped fighting each other, whether that was because one side had come out victorious or they finally got their acts together and stopped fighting to team up, I don't know."
"We were able to hold our own in the beginning, but it wasn't enough. Nine years after they started really showing up in the Milky Way, when I was fourteen, the Wraith managed to find away around Atlantis' sensors and catch the city off guard in a surprise attack. We were forced to evacuate back to earth when it became obvious that the city was lost."
"Another six years after that the Wraith finally broke through earth's defenses and devastated the planet. Out of the billions of people on earth only a little over a thousand managed to make it to safety. We've been on the run ever since."
Finished giving a basic run down of what the last twenty-four years had been like, Troy paused a moment to let everything he'd said so far sink in.
"How were you able to kill all those Wraith on the hive ship?" John inquired after a moment. Out of everything that had happened so far he found that it was surprisingly that question that had been nagging at him the most.
While they'd been waiting for Carson, John had contacted Caldwell and had him run a sensor sweep of the hive ship. The colonel had confirmed that there were no life signs that could be detected - which didn't really mean anything since hibernating Wraith didn't show up as life signs. So far all the teams that had been sent over had found nothing but dead Wraiths everywhere.
"Airborne contagion that Carson and some other scientists developed, using a combination of parts from Carson's retrovirus and parts of the Hoffan serum. It's one hundred percent deadly to the Wraith, but completely harmless to humans. "
"One hundred percent?" Carson spoke up for the first time, not liking what he'd just heard. He was already having issues with his conscience and morality over the retrovirus he'd developed to turn Wraith into humans...but genocide? No he would never allow himself to go that far...would he?
"Yeah, unfortunately for us by the time the substance had been perfected the Wraith had already attacked earth and destroyed most of earth's defense ships leaving us with no way of distributing the drug on a large scale. All off world personal carry a canister with them just in case they're captured though."
"No, I can't believe that I would willingly participate in what essentially amounts to genocide. When I developed the retrovirus for the Wraith, it was to free them from what I perceived to be an unnatural state, not kill them."
"You say that now, but I guarantee you, that you stopped giving that bullshit answer after you were forced to watch as your wife and daughter where taken and fed upon right in front of you, during that last attack on the city by the Wraith." Standing up Troy began to pace. "Every last one of us who survived that last attack changed, including you Carson. We all changed into people we never wished to become, did things we're not proud of, but we did it in order to survive, to keep the Wraith from destroying us."
Having nothing more to say Troy turned and left the room, the others were too stunned by everything they'd learned to try and stop him. He could feel all the emotions he struggled to force down everyday threatening to surface and consume him. He had to get out of there and regain his balance before he drowned in the emotional tidal wave he'd been riding since being thrown back in time.
Later that night Elizabeth sat up in bed leaning against the headboard, her knees pulled up to her chest, arms wrapped around them. Resting her chin on her arms she listened to John's soft breathing as he slept next to her. She longed for the comfortable embrace of sleep, she couldn't remember the last time she'd had a decent, honest to goodness night's sleep with out the aid of the sedatives Carson had prescribed for her. And even those weren't as affective as they once had been.
Her mind was racing with thoughts of the day's events, what had happened...what could have happened. When she thought of what would have happened if it hadn't been for Troy, of all the lives that would have been lost because of her decision - and it was her decision no matter what anyone said, in the end she always had the last say - it made her want to curl up into a tiny ball and just dissappear. An incredible feeling of overwhelming hopelessness and guilt threatened to drown her in its intensity.
Drifting into wakefulness John's sleep fogged brain registered that something was slightly off around him. Peeling an eye open he made out the shape of Elizabeth beside him, sitting with her back against the headboard and her knees drawn up. Immediately he knew something was wrong, carefully, not sure if she was aware that he was awake, John reached out to gently rub a hand up and down Elizabeth's shin.
"What's wrong?" John hated seeing her upset or hurting in any way.
Elizabeth was silent for several moments before answering, "I don't think I can do this any more."
Really worried now John sat up, wrapping an arm around Elizabeth's shoulders, his other had rubbing up and down her arm. "Do what anymore?"
She looked up, frowning like she'd expected him to know the answer to that. "This job. I don't think I'm cut out to make the kind of decisions it requires.
"Why would you thing that? You're great at your job, sure sometimes it can suck like hell, but I don't know anyone I'd rather have doing it." Kissing her temple softly, John started to soothingly rake his fingers through her hair. "Does this have something to do with what happened today?"
"God, John when I think of what would have happened if it hadn't been for Troy, of the lives that would have been lost..." She couldn't fight it off anymore, Elizabeth buried her face in John's shoulder and let the tears she'd been fighting back fall.
"Shh...I know, I know." John pulled her close, rocking gently. When her tears subsided he pulled back just enough to look her in the eyes. "Elizabeth you're one of the strongest, most compassionate people I know, and believe me when I say there is no one who could have done a better job here than you have."
"You can't beat yourself up over something that didn't happen...not this time anyway. Troy changed history, changed the timeline, the things he spoke of might still happen or they might not, but the fact is that's all in the future and we have no way of knowing what'll happen. But whatever happens we'll deal with it together when the time comes, until then all that matters is the here and the now. We just take it one day at a time, whatever's meant to happen will happen." Adjusting their positions so that they were laying down - her on her back and him on his side - John wrapped an arm around Elizabeth's waist pulling her close to him. "Now come on you need your sleep. All this worrying and stress can't be good for the baby." He bent down to lovingly kiss her stomach before settling back.
Knowing that John was right Elizabeth let out a soft sigh as she snuggled into John's warmth, grasping the hand that rested on her stomach, entwining their fingers together. Tomorrow was another day, another chance to try and make things better. She could live with that...for now.