Stargate Atlantis -:- The Collective

Summary:

An explosion rocks Atlantis with Sheppard caught in the middle, but that's only the beginning of his day-off from hell. Something is loose in the city, and it's using the residents to reach its goal: total domination. Shep-whump fest, implied Sheyla.

Setting/Spoilers:

Late Season 5, potential spoilers for any episode really

Genre/Rating:

Hurt/Comfort/Friendship/Action/Adventure – rated T to be safe

Author's Note(s):

Finally decided to take the plunge and start writing this fic; I will warn you though, that it really is still stuck in the planning stage – I've created an impossible situation, and at this point I have no idea how they get out of it – I'm going to try organic writing and see how it goes lol

On another note, this fic has a non-linear plotline with a lot of time-shifts between past and present (think 'Tabula Rasa' – great episode and inspiration for this fic) Keep an eye on the subtitles, in paticular the times, if it gets confusing – that's what I'm going to be doing :P

Okay, I think I'm done filling my word count now – Enjoy!

Chapter One -:- Concussed and Confused

(Present) 11.00am – Central Tower/Laboratory Delta29-B

Harsh light flashed against his eye-lids, easily convincing him to keep them closed. John Sheppard had hit his head enough times in the past to know that opening your eyes to bright light hurt like a son of a bitch. Even more so than the current pain that bounced around his skull like a rabbit armed with a jackhammer. He decided to try and figure out what was going on by ear instead.

After a moment of concussion-induced fogginess, he recognised the sound of sparking electrical cables – explaining the strange light flashes. You knew you had spent way too much time with Rodney McKay when you could actually identify the sound of shorting wiring. The thought of being that close to live electrics freaked him a little, but moving didn't seem like a good idea at that moment. He shifted slightly regardless only to find that he couldn't move anyway. Something heavy lay across his chest, the movement causing pain to flare up in his ribs.

Then he heard voices. They sounded miles away, but again by experience he knew them to be much closer. He couldn't make out what they were saying, but one sounded familiar and female while the other was totally foreign and male. They were coming closer, the garbled voices making intermittent sense.

"…a survivor…thrown…blast…"

"…the Voice decrees…taken…others?"

"…dead…only one…"

What the hell? John was majorly confused. He began to panic a little when he realised he couldn't remember where he was or how he got there. There had been a 'blast' so…an explosion? That would explain the shorting wiring and the major headache he was now experiencing, but what was 'the Voice'? Who were the 'others'? Was he the only 'survivor'?

John got a little fed up of trying to piece things together with his eyes closed. Cautiously, he blinked them open, to find himself in a familiar room lit with emergency lights and sparks. He recognised the décor as Atlantean, reassuring him, if only a little, that he was likely still in Atlantis. He turned his head slightly, a blurred figure coming into view above him. "K-Keller?"

Dr. Jennifer Keller didn't react to her name at all. She wasn't even looking at him, instead staring intently at the tablet PC attached to the medical scanner she was currently waving over him. A look of annoyance flickered across her features and she addressed the unknown male that John couldn't see. "He is not of the Infected."

"We have located another potential threat to The Collective," the other person replied. John tried to process what he was hearing, but nothing was making sense. "He is wearing the dress of the Civilian class. He has been assessed as a low threat level. The Voice decrees that he be contained."

John briefly wondered if they were definitely talking about him or not – he was rarely ever seen in anything other than his BDUs, but the guy had claimed he was wearing civvies. It was then that he felt the unfamiliar denim material on his legs, confirming that he was wearing jeans. He must've been off-duty when whatever happened, happened. Apparently in typical Sheppard-style he had managed to find trouble even on his day-off.

The weight across his midsection abruptly disappeared as someone outside of his field of vision lifted off the rubble pinning him. John gratefully took a deep breath, but instantly regretted it when the action set his lungs on fire. Two others dressed in the Lantis military uniform loomed into view, but they were new recruits that John had yet to learn the names of. They each grabbed one of his arms and hauled him to his feet; the pain of his injuries nearly causing him to pass out.

Now upright, John got a better view of the destruction around him. He could make out enough of the damage through blurring vision to know that it had been one helluvan explosion – he was lucky to have survived with only the relatively minor injuries he had. He caught a glimpse of a charred hand poking out from behind the remains of a console as the soldiers dragged him out of the room. John panicked when he realised that he had no idea who the hand belonged to – who had been in the room with him? What were they even doing in there in the first place? What the hell had happened; and what the hell was going on now?

Stepping out into the corridor beyond didn't help ease his confusion. At the door stood four more soldiers, all heavily armed and kitted out in full assault gear. They didn't acknowledge the presence of Sheppard's entourage, but silently stepped aside as they passed. John noted the heavy guard, filing the information away for later. Once in the hallway Keller led them down and to the left. They passed through two more corridors and took a transporter trip before John finally realised where they were going. The holding cell.

He was going to blame the slow realisation and his complete lack of direction on the concussion. It had stolen that along with his memory and his ability to move unaided.

From the transporter they stepped into a corridor full of activity. Atlantis personnel streamed purposefully up and down the hall; all of them completely oblivious to John's captivity. Sheppard blinked in confusion, wondering if he was even more concussed than he was taking credit for and was imagining the whole thing. The scene around him was just so normal it didn't fit with the wacky weirdness he had woken to. It wasn't until he took a closer look that he realised that there was nothing 'normal' about the people milling around him.

Their eyes were completely glazed over and unseeing; although their steps were sure as if they weren't being guided by mere vision. There was no noise either; none of the usual chatting or hailing – just the practically robotic march of booted feet echoing around the space. John immediately drew the similarity to a Replicator-controlled Atlantis and shuddered. God, he really hoped that wasn't what was happening.

As they continued down the hall, literally two corridors away from the cell, John was disheartened to see so many familiar faces completely ignoring him. A lot of the people passing were his own men, fully cladded out in tactical gear, P90s held ready at their chests. The others were scientists and civilians who were also armed, but only trusted with Wraith stunner pistols. It appeared that whatever hierarchy previously occurred still existed – though the soldiers now seemed more willing to do as the geeks ordered.

They turned a corner, and hope bloomed in Sheppard's battered rib-cage. "T-Teyla."

The Athosian ignored him; eyes front as she approached – her path aiming to take her around the parade surrounding him. He called out louder, even as he realised it was hopeless to reach her through whatever control had taken over. Surprisingly, she stopped; as did the soldiers gripping his arms and Keller who was leading. Apparently, Teyla held a higher rank than those arresting him, and everyone else too as absolutely everything came to an eerie stop.

Once again, John flashed to a memory of the Replicators rendered stationary by McKay's computer program. If it weren't for the fact he could see the slight flicker of their eyelids, he would've sworn that everyone had been flash frozen. He considered using the opportunity to escape, but the grip on his arms had also frozen like a vice.

Then Teyla spoke; but the words didn't sound like her at all. "New memory data received. The prisoner is of Military class; rank Lieutenant Colonel. Threat level re-assessment complete. The prisoner is a danger to The Collective. The Voice decrees that he is to be terminated."

With barely a flicker of movement, John found the business end of a 9mm handgun in his face. "Now?"

Teyla ignored his comment; though the empty click of her thumbing the hammer down answered his question.

This was turning out to be one helluva day-off.

(Past) 08.00am – Central Tower/Mess Hall

"Aren't you up a little early on your day-off?"

John looked up at the owner of the voice only to see a piled-high tray of breakfast goodies. That alone told him that Rodney McKay had arrived. The astrophysicist took the seat opposite him and rubbed his hands in barely contained glee at the feast before him. John glanced at his own forgotten half-eaten breakfast then shrugged. "I am physically incapable of sleeping past 5.53 in the morning." He answered and Rodney gave him a curious look. "A trauma from way back at Basic that I have no desire to revisit."

Rodney gave a snort as a reply, his mouth already occupied with a way too larger bite of food. John returned his attention to the tablet PC he had hijacked to complete the last-minute paperwork he was meant to have done the day before. So far he had managed to avoid Woolsey and the inevitable lecture about bureaucracy that would follow, but he knew his luck would run out eventually. Rodney slowly managed to chew and swallow his first mouthful. He jabbed his fork at John "Didn't know you owned anything other than your uniform and a closet of black t-shirts."

"Me neither," John answered, giving his outfit a glance. He had honestly been stumped that morning when he realised that he had to pick something other than his uniform to wear. He had managed to find a pair of jeans, a t-shirt and a black shirt after searching his yard-sale of a room. "Found it in the duffle I still haven't unpacked since I took leave last year."

Rodney rolled his eyes and proceeded to shovel another monumental bite of food in his mouth. Ronon and Teyla took that opportunity to arrive, each taking their seats without a word. This had been 'their' table for nearly four years now; their routine set in stone. Teyla gave Rodney an inquisitive look as she watched him struggle to chew his mouthful, then gave a small sigh as Ronon took it as a challenge and spooned in an even larger amount. Honestly, neither of them would ever learn proper table manners. She then looked at John who was still stabbing at the computer. "I thought it was your day-off?"

"So did I," John smirked as he managed to type on the tiny touch keyboard. The computer gave a congratulatory beep, and John gave her his most charming smile as he laid it down. "And now it is. God forbid I file a mission report more than a day late."

"Considering our last mission was nearly a fortnight ago, I would say it was little more than 'a day' late," Teyla gently chastised. John just shrugged.

"By my standards – this was early," he closed the file he was working on and opened a game of solitaire. Teyla had never really understood the game, but she often found the Lantis personnel playing it when they believed their superiors weren't looking. Apparently there was a competition going on where players published their scores online – Rodney was still sore over John topping his high score. Without looking up, he picked up on the one person missing from the table. "Where's Torren?"

Teyla smiled like she always did whenever she thought of her son. "Dr. Keller wanted to spend some time with him before he goes to New Athos this afternoon. Kanaan is expecting us after noon."

Teyla didn't miss the slight shift in emotion on John's face, although the two men having the eating contest opposite obviously did. She never knew what to make of the odd expression he had whenever she mentioned Kanaan; it was usually gone the same instant it appeared. Some small part of her hoped it was jealousy – had he finally realised that there was something more than mutual respect between the two of them? In all the years she had known John, the only time he had ever made a move was when he was under the influence of the iratus retrovirus. Truthfully, she had never made a move either, but that was the way of her people.

It was too late now anyway. Even thouugh the relationship between her and Kanaan had been strained by the distance between them; they had a son, and Teyla would always do what was best for Torren.

The look was gone now, John's typical cavalier expression propped back in place. He was still focused on his card game, his eyes never meeting hers. Teyla briefly wondered if he was distancing himself from her on purpose; his respect for her outweighing any other feelings he may have. The logical part of her was grateful. If either of them acted on feelings neither would admit, she doubted she would be ready for the complications that would follow.

The silence was broken my Ronon's celebratory cheer. McKay threw him a look over reddened cheeks as he spluttered slightly. As it turned out, the unspoken rule of the challenge was that the victor was the one who ate the fastest without choking. Rodney, having choked on a rather large bacon rasher, had ultimately lost. Teyla laughed along, but her thoughts were still stuck on the man sitting next to her.

"So, what are you gonna do today?" Ronon asked Sheppard, his eating pace significantly slowed now that he had won. Even Rodney was taking his meal at a more cautious rate having learned his lesson.

"I fully intend to do absolutely nothing," John answered. He smirked at Rodney across the table, and then held up the tablet PC. Once again he had trumped McKay's score by a landslide. The astrophysicist, completely unprepared for taking two defeats in the space of five minutes just huffed irritably. He would get his revenge on both men later. "Though apparently, that isn't going to happen."

Teyla followed John's line of sight to see Major Lorne making a bee-line towards them. He paused at the edge of their table, his expression apologetic. "Sorry sir, but there's a problem in one of the labs…"

"It's not the laptop thief again is it?" Rodney interrupted. John rolled his eyes while the others looked confused. McKay had enlisted his help the night before in tracking down the elusive thief that had stolen his laptop that was somehow preciously different from every other on Atlantis. It turned out that a new recruit had borrowed it by accident, though Rodney was nowhere near forgiving the error.

Lorne shook his head to cover his own confused expression, and then continued. "Dr. Fredericks wants to talk to his marine details' superior following some mishap – apparently, being acting military commander isn't good enough."

"I doubt being actual military commander will do much good either," John shrugged as he stood up. He had dealt with the uptight scientist before on multiple occasions. It was never a fun experience. He gave one of his small waves as he followed Lorne out of the mess hall, leaving the others behind.

Rodney watched them go, and then glanced at his watch. Immediately he hopped to his feet, stealing John's abandoned computer, and moved to leave as well. At Teyla's curious look, he felt he maybe should explain himself and so paused in his escape. "Carson comes back from M34-J82 today. He's gating in at 8.30 and I said I'd meet him. Before I go and do other far more important things of course."

He covered before he hurried off. She always found it strange how Rodney would rarely admit that he actually cared about other people. Carson was his best friend, she knew, but still he had to cover the fact that he was excited to see him for some reason. Teyla shared a look with Ronon as they finished their breakfasts.

Between computer card games and weird social behaviour she doubted she would ever fully understand the Earth people.

(Present) 10.40am – Central Tower/Level 25 – Section Delta

Okay…ow.

So it wasn't the most eloquent just-woken-up thought he had ever had, but it pretty much summed up the way he felt. Major Evan Lorne found himself sprawled on his stomach, arms splayed as if at least some conscious part of him had decided to break his fall. Gingerly, he rolled himself onto his back, trying to piece his pre-passing out thought processes back together.

There had been an explosion, he knew that much. A lab up on the 29th level of the delta section of the central tower had suffered some major malfunction that in true Pegasus-style ended with something going boom. He had been on his way to the hot zone, yelling instructions over his radio when all of a sudden the world tilted sideways. Lorne briefly berated himself – he'd only been acting military commander for a few hours, and he'd ended up fainting in the middle of an emergency.

But this wasn't the time. There were far bigger things than why he had ended up on the corridor floor; say for instance – a massive explosion. He checked his watched as he climbed to his feet, again rebuking himself when the corridor spun a little, worried by the fact that it had been a whole ten minutes since the emergency call had been made.

"This is Major Lorne, I need a sit-rep from the hot zone."

Static. Okay, he knew he'd missed the last ten minutes, but that was no reason to give him the silent treatment. He tried again, injecting as much authority into his voice as he could – he was the man in charge after all. Still, there was only silence in his earwig. He tapped the radio twice experimentally, a reassuring click confirming that the device was indeed working. It was just that nobody was answering. Something was definitely not right.

Well-honed senses were then on alert. He was only four floors down from the hot zone and yet there was no noise. There should be shouts and questions, the calls co-ordinating the response over the radios and the thrum of machinery as necessary. And yet there was just an eerie silence. The complete lack of activity was making Lorne feel very alone. He unclipped the top of the sidearm holster on his thigh.

"This is Major Lorne, does anyone read?"

He tried again as he continued towards the transporter at the end of the corridor. There were hundreds of personnel on Atlantis then – how could none of them be responding? The lights were still on and the transporter door opened at his command, so they still had power. That was usually the first thing to go if they were under attack. Yes, he was thinking worst case scenario, but what else could explain the complete silence?

He selected a dot on the transporter screen that would take him up to the hot zone floor. With a flash of white light that he barely noticed anymore, he was teleported higher into the central tower. The doors opened with their usual whoosh, and suddenly Lorne found himself in the middle of the most ordered chaos he had ever seen.

Compared to the emptiness of his previous location, the corridor he now stepped into was practically teeming with activity. People he recognised, along with new recruits that he didn't, streamed around him, not one pair of eyes meeting his. It was disconcerting to say the least. Considering he was literally around the corner from the hot zone, the silence in which everyone moved was beyond odd. "Hey! What's going on?"

Evan Lorne had never been so completely blanked in his life – and he'd been the arty-type in high school. If he thought there was something wrong before, he knew that something very Pegasus-Galaxy-weird was happening now. He pushed through the crowd that managed to always get in his way until he found a very familiar face. "Henson!"

The young lieutenant who had been on his gate-team for nearly four years ignored him. Lorne was getting a little bit irritated by the lack of co-operation. He grabbed Henson by the arm, effectively halting his progress, and spun the young man round to face him. "Henson! What the hell is happening?"

Lieutenant Henson blinked very slowly, though his eyes remained unfocused. He removed himself from Lorne's grip and studied his superior officer. Lorne watched as recognition slowly dawned on the young man's face, though it turned out not to be the recognition he wanted. "You are not of the Collective."

"Excuse me?"

All around them, all activity ceased. Everyone went from completely ignoring Lorne, to now staring intently at him. He almost missed being practically invisible. It was weird how they all moved as one, and yet at the same time acted independently. Their movements were almost robotic in nature, while their blank expressions reminded him of mind-controlled zombies. Seriously – what the hell was going on?

"You are of Military Class; rank Major. You have been assessed as a threat to The Collective," Lieutenant Henson said in monotone. Lorne really didn't like where this was going, his eyes already searching for an exit as his hand went for his sidearm. "The Voice decrees that you are to be terminated."

Oh, so not good.

Henson lifted the P90 clipped to his vest as Lorne drew his sidearm.

(Present) 10.50am – Beta Tower/Laboratory Sierra74-F

Life in the Pegasus Galaxy is pretty tough for brilliant scientists; especially with both sleep and coffee being rare commodities. It generally led to said brilliant scientists catching some shut-eye pretty much wherever they stood, or preferably, sat. As such, Rodney McKay – self-proclaimed as the most brilliant of said brilliant scientists, had often found himself waking up in the oddest of places. Hence why he wasn't greatly surprised to find himself bent at a perfect right angle at the waist across a desk; his feet on the floor while his upper body squished his laptop flat.

It was right up there in the Top-10 weirdest positions, but it definitely wasn't number one. That was reserved for an especially scarring wake-up he'd prefer to forget.

With a disorientated grunt he pushed himself up and back, promptly falling into a chair he had forgotten was there. He was immensely grateful for it – the floor was probably even less comfy than the desk. He blinked around him, trying to remember whatever was going on before his cat-nap. He was in a lab, but not his one. He briefly remembered his actual lab being commandeered for some test or other that was completely beneath his intellect, leading him to search out another sanctuary. Apparently, this shoebox of a lab had sufficed enough at the time.

He leaned forward automatically to grab at his omnipresent coffee mug, only to find it absent. Confused, he leaned forward in his chair in a half-hearted search for the precious caffeine. He was very disappointed to find it on the floor, the contents spilled in an impressive puddle – he'd barely had a sip before…

Before what? When had he dropped…?

The explosion.

"Sheppard." Rodney muttered, his eyes widening as the shards of memory finally slotted back into place. Lorne had called over the radio that there had been an explosion in Lab Delta29-B – a lab that only twenty minutes before had required an ATA user to act as a human light switch. Rodney had laughed as he eavesdropped on the conversation where John had been bullied into helping out – it was his day-off after all, it wasn't like he was doing anything. And now…

"Please don't be dead," Rodney whispered. He'd lost too many best friends; he didn't think he could handle another. In fact, he was pretty sure the only reason he was managing was because he had had John to help him through. Steeling himself with a deep breath, Rodney tapped his earwig. "This is McKay – any word on the explosion?"

He was expecting an impatient, automatic answer from whoever had been put in charge of fencing panic calls. What he got instead was nothing. Just the dreadfully empty hiss of static. "Hello? Does anyone read?"

"Oh thank God, Rodney! I've been trying to get a hold of anyone for the last five minutes!"

"Carson?" Rodney answered, slightly confused. Shouldn't Beckett be at the lab helping the survivors…if there are any? He shook his head against his own thought, instantly regretting it when a headache made itself known. "What the hell is going on?"

"I have no idea," Beckett replied, sounding just as bewildered as Rodney felt. "I got the call about the explosion – then suddenly I woke up on the infirmary floor with Captain Burton hovering over me declaring me a low threat or something. He tried to arrest me, broken arm and all. I had to sedate the poor lad for fear he'd do himself more harm."

Now Rodney was really confused. "Wait…'low threat'?"

"I don't have a bloody clue. He said I was a 'low threat' to some collective or other because I was a civilian. He was on some pretty strong pain meds."

"Have you been able to contact anyone else?" Rodney asked, deciding that the high marine was irrelevant to their current situation. He was more concerned with what was actually happening, not what some drug-induced grunt thought was happening.

"I heard Major Lorne on the radio about five minutes ago, but I was a wee bit busy wrestling my one-armed patient. I tried to call him back but I got not answer."

Worrying, to say the least. It didn't seem that anyone was at all concerned about the explosion. And for some reason no one was using the radios either, well, at least not for long anyway. Something was definitely going on, and it was nothing good.

"Okay, it doesn't sound like help is getting to the lab where the explosion occurred, so it makes sense that we should head there. There are probably survivors that are going to require your voodoo" like Sheppard, he thought, but feared voicing his concern would make it valid. "We'll meet outside the transporter on level 29 in delta section. It should only take about five minutes."

There was a pause over the line, and Rodney knew that the doctor had nodded, obviously forgetting that he couldn't actually be seen. "Right. I'll see you there."

McKay signed off the radio call; made a last ditch attempt to hail anyone else, then collected up the tablet PC he had stolen from John that breakfast. He had practically broken his laptop in half when he had collapsed on it, and besides, the tablet was more portable. At the door he took a deep breath before waving his hand over the control. He honestly had no idea what he would be stepping in to.

Thankfully, the corridor beyond was completely clear. That wasn't unusual – the beta tower was a far lower traffic area than the central tower; the quiet was probably why he had selected it for his temporary lab. Even if it was miles away from key places; say the mess hall and its vital coffee machine.

Soon, though, the quiet became very eerie. Yes, the beta tower was usually pretty scarce of people, but it was never this empty. Rodney found himself clutching the PC a little tighter, as if that would actually help him. His pace slowed to an extremely cautious and tense walk, his eyes darting nervously into every dark corner. He had no idea what he was afraid of, but he found himself jumping at shadows regardless.

That was probably why he jumped sky high when he actually did meet another person.

"Zelenka! Thank god!" Rodney gasped. He then quickly hid his previous fear and present relief under a well-rehearsed disguise of arrogant indignance. "You scared the crap out of me! What do you think you're doing prowling through the corridors like some kind of ninja assassin? You realise there are other people around who don't really appreciate being jumped out at. Seriously, if you're going to lurk, at least wear a bell so the rest of us know you're coming!"

Zelenka stood completely still throughout the whole spiel. He fixed McKay with an unfocused stare. When Rodney finally paused for breath and looked at the scientist properly, he realised there was something distinctly odd about him. The way he just stood there was unnerving Rodney to no end. But it was worse when he spoke.

"You are not of The Collective."

"Collective…?" Rodney remembered what Beckett had said about the high marine. Captain Burton had then attacked Carson following that statement. Rodney looked in Zelenka's eyes, but the Czech scientist wasn't looking back. Something really weird was going on. "Oh no…"

"You are of Scientist class. Your threat level has been assessed as low. The Voice decrees that you are to be contained."

McKay caught the briefest glance of the wraith stunner in Zelenka's hand, and then he turned tail and ran. At that moment, Rodney was incredibly grateful for the last five years he had spent on Sheppard's team – it had taught him to run really fast. The first shot hit the wall behind where his head had been, but he was already half-way down the hallway, doing his best to not panic.

The funny thing was, he was Rodney McKay, and he had a tendency to panic.

Flashes of blue sputtered around him as he began a freaked monologue under his breath. The stunner, though technically harmless to him, was still made of kinetic energy that blasted the corridor around him. Still talking, his main defence mechanism, McKay kept running. He took every turn he could see – already completely lost, but that didn't matter as long as it lost his pursuer too.

Eventually, the stunner blasts got fewer and further away and McKay allowed himself a moment of triumph when a transporter came into view. He skidded to a stop in front of the door and was just about to wave his hand over the control when a tell-tale flash of white shone round the frame. The doors opened to reveal two well-armed marines.

"Are you homicidal zombies as well?"

The twin stunner blasts to the chest answered that question.

Woot! I finally finished this chapter. I started and abandoned it at least twelve times lol. I hope it isn't too confusing, I'm going to start actually answering the 'what the hell?' questions that every character has so far asked next chapter…

Please let me know what you think!