A.N: I have written this story because I wanted to explore how the individual characters might deal with a long period of isolation, and to do this I have had to make the virus that threatens Atlantis much worse than the Coronavirus. This is not to scare anyone, but simply because, in such a small, controlled society, Coronavirus would not have been enough of a threat, and wouldn't have required the characters to be separated from each other. Anyway, there is humour amongst the angst and I hope you enjoy it.

Chapter 1

Up the stairs and along the gantry, his boots ringing on the metal surface, their beat steady and sure. He increased his pace on the straight, feeling his lungs beginning to strain, the muscles in his legs burning, the sweat dampening his shirt. Faster, as the gentle curve turned downward, and on toward the corridor that would lead him home. A sprint to the doorway, before his cool-down jog; legs pumping, eyes on his goal, the burst of power exhilarating. Nearly there.

The door slid shut in front of him and, in his mind, John felt the finality of its closure; locked and sealed. He skidded to a halt.

"Dammit," he gasped, without any particular surprise or annoyance. He turned and jogged back up the walkway, turned again, jogged and so on, until his breathing was calm and steady once more, then he stopped, did some stretches, walked up and down a bit and then finally sat down against the wall and waited. Silently and alone, John waited for Atlantis' decontamination cycle to complete.

Two Weeks Earlier

Rodney had decided, for a change, and because there was no particular crisis involving imminent death and last-minute saves, to get a good night's sleep. He wasn't impressed, therefore, to be rudely awoken by the citywide alarm when he'd only just dropped off, and even less impressed, when he fumbled for his squawking earpiece, to have Sheppard yelling urgently in his ear.

"McKay! Rodney!"

"What?"

"The City's locked down! We're in quarantine!"

"Why? What happened?"

"Sergeant Cruz's team Gated in and all the doors locked. Something's going on with the air-con too."

Rodney sat up; where normally he would have felt a soft, almost imperceptible breath against his skin, the air felt still and dead.

"McKay?"

He scrambled out of bed, tripped over his boots, and brought up the lights.

"Sounds like the airborne diseases protocol," he said, sitting down at his desk and tapping his laptop to life, all vestiges of sleep suddenly gone from his mind. "Are any of the team sick?"

"Control says they don't seem to be."

"Where are you?"

"In my quarters. Locked in, like everyone else!"

Rodney could hear the frustration in John's voice and knew he'd be pacing up and down like a caged tiger. He brought up a display.

"Yes, here it is; airborne diseases protocol, which means immediate lockdown and a negative pressure environment in the affected areas."

"And then what? We can't just sit here doing nothing!"

"And then it's up to the operator, that is, yours truly, to enact the next stage."

"Which is?"

"To allow a safe route for key medical personnel to get to hazmat storage, and from there to the affected area. Then to create a negative pressure route from there to the infirmary."

"Great. You can unlock my door while you're at it."

"No, I can't."

"McKay! Let me out!"

"No, I mean, I really can't. You know we've had issues before. I've done a lot of work on this, writing macros that will take over, and making it tamper-proof. The City's in control now."

"C'mon, Rodney, you must have left a back door!"

"No, Colonel! Airborne disease? What could you do, even if I could let you out, other than a great deal of damage? Now, shut up and let me work!"

oOo

John paced. And waited.

"Colonel Sheppard?" Woolsey's voice.

"Sheppard here."

"I'm afraid I have bad news." Woolsey's tone was grim. "I've just heard from Dr Keller." He paused and John felt his heart race. "Sergeant Cruz started showing symptoms on the way to the infirmary. And... and she died shortly afterward."

"Died?" John was stunned.

"Her temperature spiked, she collapsed, and then there was massive haemorrhaging."

The rest of the team? The Gate techs? The Marines?"

"Keller is monitoring them closely, but they're showing no symptoms as yet."

"Maybe they won't, maybe..."

"Colonel... Dr McKay informs me that Atlantis' system recognised the virus."

"Yes, he told me." John heard a sigh in his ear.

"The type seems to be one of a group that has a very high fatality rate and a potentially long incubation period."

"But Cruz..."

"Potentially long, which means it can vary significantly between individuals."

"Has Keller confirmed it?"

"No, not yet. But..." Another pause. "Colonel, we could be looking at months of quarantine."

"We can't just stay in our rooms and starve!"

"Dr McKay assures me that it's feasible, that the protocols are in place for individual door locks to be released periodically and that the Atlantis systems will keep people separate and decontaminate corridors and rooms after use."

"Some people are in groups, sharing quarters." There was no reply, so John drew his own conclusion. "If one goes, they all go."

"Sadly, yes."

"It might not be that bad. The system might have glitched."

"Let's hope so, Colonel. Woolsey out."

Months? John thought. Months alone, isolated? For a moment, he envied the Marines in the shared quarters; but would that be worse? Confined for months, together? He thought about some of the characters he'd shared barracks with over the years; some of them would have driven him crazy. Questions flooded into his head; the logistics of separating the whole expedition, hundreds of people. Would the system allow for exercise? Let a few out at a time, keep them apart? Ronon - he'd break out no matter what; you couldn't keep a man like Ronon shut up in a small space for long. John was heartily glad that Teyla and Torren were away on New Athos. He wondered if the Gate would work; surely Atlantis would let them dial out, with the shield up, so they could communicate? They needed to let Teyla know, and Earth. Thoughts teemed in his head: the what-ifs, the whys, the whens, the hows. His pacing grew faster and he linked his fingers behind his neck, feeling the muscles ache with tension.

Then John stopped and closed his eyes. He let his arms fall to his sides and allowed his shoulders to sag, imagining tension draining away from them and dripping out of the ends of his fingers. He breathed slowly and his thoughts calmed.

Months. Who needed to think about months? Or weeks, or even days? It was too big, too much; all John needed was to know that at this time, in this present moment, all was being done that could be done, to safeguard all of the personnel on Atlantis and to stop this disease spreading anywhere else - to the Athosians, to other allies, to Earth. John wondered about the planet that Cruz's team had returned from. It had been a peaceful first contact mission to another of those typical Pegasus societies; small, agrarian, size and technology limited, as usual, by the Wraith. Anyway, it didn't matter; all that mattered was to do what was necessary, right now.

"McKay, what's happening?"

A pause, then Rodney's voice, flat and emotionless.

"It's done. I've enacted the lockdown protocol, allowing for the current whereabouts of all members of the expedition: access to food, limited exercise, negative pressure routes for medical staff, decontamination procedures."

"It's confirmed, then?"

"Yes," Rodney replied, tightly. "Jennifer ran the bloods. It's in the Ancient database. Rare. Incredibly infectious. Almost always lethal. We'll have to hope the isolation procedures kicked-in as soon as they came through the Gate, or..." He trailed away, leaving John to imagine the consequences.

"How long will this last?"

"If it got into the air supply... Well, it's a 'tricky little bugger,' as Carson would say; it could be up to five months before it shows up in blood tests or symptoms."

"Five months! What about the Gate? Can we let Earth know? And City systems? Can we run everything?"

"Yes, John, it's all rerouted to me," said Rodney, tiredly. "And Woolsey's telling the SGC now. He's already spoken to the Athosians."

"Did he talk to Teyla?"

"No, it was Halling. Ah, the Gate's shut down. I'll drop the shield." John heard the tap of Rodney's laptop.

"So, now what?"

"Woolsey'll do a citywide, tell everyone. Then... we wait."