Chapter 2: Atlantis

Consciousness wasn't exactly something he wanted to experience at this point.

Knives were jabbing themselves into his brain, pulling it apart piece by piece, until individual thoughts were like barely grasped shadows.

It was worse than being fed on by a wraith.

Claws in his chest, pulling his lungs out.

Knives driving deeper with every breath. Every muscle twitch.

He tried to roll over, to bury his head away from the lights which were only making things worse, but that… didn't work so well.

"Colonel Sheppard!"

"John–"

He groaned, trying – unsuccessfully – to swallow down the sudden pain and nausea.

And to drown out the incredible cacophony around him.

He wasn't successful.

"Beckett, get in here!"

Rodney.

He screwed up his face, trying to block out the minuscule amount of light that was leaking in between his eyelids. Too much.

"Easy there, what's all this then?"

It was too much.

Too loud.

Too much sensation.

Not enough darkness.

He really couldn't be responsible when everything crashed down on each other and he promptly lost his lunch. At least he was probably in the infirmary already.

It sent everyone into even more commotion and it was all John could do to keep himself together. He couldn't open his eyes. His every joint felt like it was on fire.

He would give anything for it to just stop.

"I'm just going to give you something for the pain," Beckett's voice sounded far away, but John was ready to take anything at that point.

Ten minutes later and he had been moved into a room that was significantly darker and quieter, and whatever painkillers Beckett had shot him up with were starting to do their job. John wasn't about to open his eyes to find out how well though.

"Colonel?" Dr. Madsen.

Right.

Because Beckett was no longer in charge of things around here. And anything that took out the colonel of the base was likely to draw the attention of the Chief Medical Officer.

"Mmph?"

"You should stop feeling the worst of the effects in the next several hours."

Worst of the effects.

Effects of what?

The effects of whatever alien was trying to burrow its way into his brain?

"Drs McKay and Zelenka are working to see how the prototype has been modified and if we need to worry about any further… side effects."

Prototype.

Prototype of what?

Was this one of Rodney's toys that had taken him out?

"Yes, yes. Side effects that he's just going to keep mulling over if you don't leave him alone with your wonderful bedside manner." Rodney's brashness grated on his tender nerves, but it was also a welcome reprieve. "If your lackey hadn't been so convinced that the warnings from the SGC about PZS were unfounded, we would've saved him a lot of pain and suffering. Now, shoo."

"Dr. McKay–"

"Look, he's alive, breathing, and no longer throwing up from the pain – no thanks to you. Besides, I believe Dr. Beckett had some images for you to look over."

There was a sharp harrumph before Dr. Madsen swept out of the room and shut the door behind her.

John let out a long breath, trying to convince his to muscles relax. His eyes were staying shut for an indeterminate amount of time.

Maybe forever.

There was a slight shuffling sound as Rodney dropped into the chair beside the bed and then infrequent taps as he no doubt worked on whatever the problem was on his data pad.

Whatever had happened.

Whatever had left him feeling like he was dying from the inside out.

"Rod…ney…?"

The tapping paused abruptly. "Colonel?"

John would've rolled his eyes if the motion didn't immediately make him sick to his stomach. "What–" He rolled the words around in his head, trying to aim for the best emphasis in as few words as possible. "–the fuck happened?"

"Eloquent as always."

John would've growled at him, if he had had the energy. As it was, he felt only marginally less like mush now.

"Well… mind you, we're still trying to piece things together, but Private Higgins decided that kidnapping the commanding officer was a wise decision and got you with a Trust-modified zat. You've apparently got the unique genetic combination that results in PZS."

The fuck was PZS?

And Rodney certainly didn't deal with any of that medical voodoo.

"Dr. Madsen assures us that you'll be back to your normal self in a couple of hours."

This time, John couldn't hold back a snort. The pain was already starting to subside from the worst – he could think in full sentences now – but even then, he couldn't imagine it just ending. Not in a couple of hours.

There was an ominous creak as Rodney shifted in the chair. "Ronon's keeping an eye out that no one else tries something, Major Lorne and Teyla have Private Higgins in the brig, and Zelenka is already taking apart the zat and sending me the specs. We've got everything covered."

John let out a long breath, because, yeah – his team was looking out for him. He licked his lips. "Woolsey?"

Rodney huffed. "Not arguing with Lorne, thank goodness."

At least that wasn't a battle he would have to deal with – but there was probably something else of equal importance that Rodney was hiding from him. John tried to crack an eye open, tried to get a glimpse of Rodney's expression, but it felt like the knives were being shoved back through his eyeballs.

Rodney poked him in the bicep. "Go to sleep John, you look like shit."

He had some choice words for Rodney, but… talking took far too much effort. Perhaps a nap would help.

"I got shot, Rodney. Shot!"

"Well yes, but you're fine."

John spun and glared at him. "Now."

"There's nothing saying that getting hit once would be as bad." Rodney crossed his arms, looking stubborn. "You were shot multiple times."

"Yes, and how was that, Rodney?"

He had been shot with a zat – a device rarely seen in Atlantis in the first place. Everyone knew how they worked though. One shot, stun. Two shots, kill. Three shots, disintegrate. At least, that was how the Milky Way variety worked. Apparently, things were different here in Pegasus.

It made him thankful that Wraith stunners were just stunners. And though Ronon's blaster did have a kill setting, getting shot multiple times while it was on stun wasn't likely to kill someone.

"I'm not getting you more of those in my city." Not when there was even the slightest chance that someone might wing him with one. It had knocked him completely on his ass for an entire day.

"You saw how little priority the SGC has for those zats though," Rodney insisted, shoving his data pad in front of John's nose. It was too close to truly make out any of the words, but the intent was clear. "They've hardly researched it! Just decided that some people have this, this… post-zat syndrome and leave it at that!"

John pushed the data pad away and kept walking down the corridor. "They've had more pressing concerns with the Trust trying to take over the IOA. Which, might I add, is a bigger problem than these little zats." As much as he disliked the shenanigans the IOA got up to, John knew that if the Trust managed to take over, things were going to get a lot worse very quickly.

He had no doubt he would be one of the first deposed from his position – there was already very little love lost between him and the IOA committee.

"Which is exactly why I need to study it." Rodney pushed forward, until he was blocking John's path. "If we get more Trust agents barging in here, what good is a military commander when one little shot will take him out?"

John grimaced.

It wasn't like it hadn't been on his mind. All it had taken was one shot from behind.

If news leaked to the Trust that he was susceptible – and there was no telling how many Trust spies they still had in the city – it would be a surefire way to take out one of their largest adversaries in Atlantis.

John swiped a hand over the nearest door sensor and dragged Rodney out onto the balcony. A breeze kicked up over the water, providing at least a semblance of cover to any prying ears in the walls. "Private Higgins had one zat, no sign of other devices on her person, and nowhere near the brains to modify it herself. She was working with someone." Someone who was most likely still in the city somewhere, passing under their radar as a regular grunt or scientist. "The last thing we need are more zats running around the city."

After all, since no one knew what caused post-zat syndrome – PZS, according to Beckett – an untold number of personnel in the city could be affected.

"You suspect my scientists?" Rodney demanded.

John raised an eyebrow in his direction. "Yes," he deadpanned, "I suspect anyone." There had been enough times over the past years that the scientists had had less than ideal motivations. The marines tended to stay out of it, but Private Higgins demonstrated that anyone could be swayed to the Trust side.

For years, John had felt more or less safe from the Trust while out in another galaxy, but the past twelve months had shown that anything was possible. The Trust was consolidating its base and was focusing on very specific targets. The Chinese and Egyptian representatives had been revealed as Trust plants only three months earlier. The American representative had been under investigation and then subsequently assassinated.

Someone was being both careless and covering their tracks meticulously.

"Make do with what you have," John said, turning to lean against the railing. "And make sure it's someone you trust implicitly. Zelenka, Kusanagi."

Rodney's lips pressed into a thin line, clearly unhappy with the ultimatum. "And if we make progress before you leave?"

John shrugged. "You've got two days."

Rodney huffed, before heading back into the main corridor, already contacting Zelenka on the comms. John had little doubt that they would make some sort of progress before he left, but he needed a really good reason to try pitching the request to the IOA. The meeting he was going to have with them was going to be bad enough.

The Trust had, once again, infiltrated Atlantis and John was helpless to actually do anything except sit back and wait for them to crawl out of the woodwork.

Even the kidnapping attempt hadn't provided any real answers. Private Higgins had gotten John when he was leaving for the morning meeting – he had been running late, so everyone else had already cleared out of the halls. Higgins had gotten him from behind and the rest was history.

Not showing up for the meeting was immediately noticed, but it had still taken two hours before Ronon had found him and Higgins in an old, unused lab space. There was no telling how many times he had been zatted, but conservative estimates suggested at least five times.

Unheard of until the modified versions started appearing.

Private Higgins had remained surprisingly tight-lipped about the entire ordeal, offering no explanation or excuse.

It was a good thing that John was already heading earth-side in a few days – they weren't going to have to wait until the Daedalus returned to send her back to earth for questioning.

Unfortunately, it meant he was going to be away from the city for nearly a full month. Who knew what kind of catastrophe the people here would manage to find in that time.

The whole purpose of his earth trip though was to prevent what had happened with Higgins. General O'Neill had cleared him to come personally vet the incoming recruits. And while that wouldn't necessarily weed out any well-entrenched Trust plants, it would hopefully be enough to instill some more confidence in the troops.

Rodney had been less than pleased that they were getting more military and not more scientists, but… it wasn't like John controlled that.

There were also rumors that O'Neill had handpicked some British special forces to appease the IOA, which were a sight better than the Germans that had been picked the last time. There were plenty of British scientists already – so no culture shock.

The radio clicked in his ear. "Colonel Sheppard?" Major Lorne's voice cut through his thoughts.

"Sheppard here."

"We've got a situation down in the brig."

Of course.

"I'll be right there."

John pushed away from the railing and headed back inside. There were more than enough problems on Atlantis to keep him occupied, without worrying about what the Trust may or may not do. But then, that's what he got for being in charge.