Chain of Command

By Flossy

Disclaimer: The following story is a work of fan fiction, and as such is for fan enjoyment only. All recognizable characters/settings are the property of their respective owners. No copyright infringement is intended, and no profit is made. I'm afraid that despite wishing that I did, I don't own these characters. Not even my muses' voodoo could make them mine (and believe me, they used a LOT of chicken blood and other such occult doodads), nor could my militant blue badgers. DO NOT MESS WITH THE BADGERS. Still, I suppose that having the boys out on loan for a while is better than nothing…

Summary: Episode Tag to 'Rising'. John Sheppard begins to adjust to his new life as the military commander of Atlantis

Central Character(s): Rodney and John.

Category (ies): Humour, friendship, episode tag.

Placement: Season One.

Rating: PG.

Spoilers: 'Rising'.

Author's Note: This is the first in my 'Aftermath' series, which, by all accounts, is going to end up pretty long. Anyways, this is kind of a cheat, as it's set after Rising but contains a short missing scene from 'Hide and Seek', but I'm sure you won't hold it against me. I have an army of highly trained blue badgers at my command, and they get real mean at times.


Major John Sheppard found himself wandering down one of the many corridors in Atlantis, not really caring where he was going. The young Air Force man had given up on the terrifyingly large amount of paperwork that was currently threatening to eat his office – it was probably going to breed and start plotting to overthrow the human residents of Atlantis – but he couldn't face sitting at that desk any longer. John knew he'd have to get it done at some point, but… He was not a paperwork kind of guy. (And the whole 'having an office' thing was creeping him out. There was a desk and swivel chair… and even a Goddamn inbox and outbox. Yuck.) Guns, impossible rescues, explosions, flying cool alien spaceships, no problem. Organising Gate teams? It brought him out in a cold sweat.

Sheppard was the first person to admit that he was deep in unknown territory – just mere weeks ago, he would have laughed at the notion of travelling through a wormhole to a different galaxy and said it was like something out of Star Trek. But that was before he'd flown General O'Neill to the research post in Antarctica and been shot at by some kind of alien missile.

It was before he'd sat in that damn chair.

The whole thing had lit up like a Christmas tree and everyone (himself included) had been astonished to find that John Sheppard, a Major with a severe black mark in his service record, possessed a rare gene. Even more amazing was the ease with which he'd been able to access the Ancient technology – and that really surprised him. He could still remember the conversation he'd had with Dr Carson Beckett, who, he'd found out, had been responsible for firing the drone…

"They think the gene was used as a sort of genetic key, if you will, so that only their kind could operate certain dangerous and powerful technologies," Carson explained, somewhat relieved that the pilot hadn't decked him on sight after his unfortunate 'accident'. Next time Rodney wanted a guinea pig, he was going to lock himself in the bathroom.

John poked the arm control panels of the chair tentatively, as if he were afraid that the thing would explode. "So some people have the same gene as these Ancients," he said, walking around said chair with a kind of morbid curiosity.

"The specific gene is very rare, but on the whole they look very much like we do," Carson continued, warming to the subject. "In fact, they were first. We're the second evolution of this form, the Ancients having explored this galaxy for millions of years before… Major, please don't," he added as he saw John start to sit down.

"Come on – what are the odds of me having the same genes as these guys?" Sheppard asked as he sat down.

The chair immediately lit up and reclined, much to both men's surprise.

"Quite slim, actually…"

Quite slim, yet here he was in the Pegasus Galaxy. He'd almost decided to decline Dr Weir's offer to join the expedition – almost. After his long and very cold exile in Antarctica (a place he found that he liked, oddly enough), it had been nice to have a half decent conversation with someone, even if it was about Stargates and aliens. A toss of a coin and his life had been changed forever.

The last thing he could have imagined when he stepped through the Gate was to end up as the military commander. That was supposed to have been Col Sumner's job, not his. He was meant to be the one taking orders, not giving them and the way he'd gotten his instant promotion would haunt him until the day he died.

It seemed that almost everything in this galaxy was screwed up.

His rescue mission had resulted in the death of his CO (by John's own hand, no less) and the awakening of the Wraith – an undeniably hostile, insanely aggressive alien race that refused to stay down when dead. John still wasn't sure which he was more afraid of – life-sucking alien vampires or the prospect of commanding the entire military contingent of the city. Still, Elizabeth seemed to have faith in him and she'd already told him that he'd be getting his very own team. It was yet another thing that the Major was trying very hard not to think about too much, but a little voice in the back of his head kept nagging at him to get it over and done with.

Him, in charge of an off-world team – Atlantis' premiere first contact away team, no less. John was still struggling to get his head around the idea and even worse, he had no idea who to pick. No, actually, that wasn't strictly true – he'd already decided to ask Lt Ford to be his 2IC. The kid seemed like a good bet – sure, he was young and still had a lot to learn, but he followed orders and had a good sense of humour. He also seemed to have a kind of inner core made of steel. Not many people would remain so calm when facing an enemy as intimidating as the Wraith, not even the most battle scarred and seasoned soldiers, but Aiden had kept his head. He'd also saved John's ass, which in the pilot's book meant that he was okay.

The fact that he had a worrying yet impressive amount of knowledge about C4 didn't hurt either.

The next place would have to go to Teyla – they needed someone who knew the area and the locals, and who could find them trading partners. The expedition had only been able to bring so much with them, and while there were plenty of MREs at the present time, John knew that it was only a matter of time before their supplies either got low or ran out entirely. Anyways, the Athosian was a damn good fighter and as the leader of her people, she was strong, physically and mentally. She was also a diplomat and he'd need someone like that.

Besides, if SG-1 could have Teal'c, he got Teyla.

The last place was much, much harder. Common sense told him to pick someone from the science department, a geek who'd be able to deal with the technical stuff, find ZPMs and so on. The problem was, John had no idea who to choose. And, if he was honest, he wasn't filled with warm fuzzies about having a civilian on what could be dangerous missions, but he pushed that thought aside. He needed a geek – after all, they were the best chance of finding a way back to Earth.

He glanced around as he turned a corner, finding himself outside the labs. Figuring he'd take a look to see what the boffins were up to (and maybe sound a couple of them out), he waved a hand over the door sensor, grinning like a kid when they swished open.

That would never get old.

The place was more or less empty, save for one figure hunched over a laptop in the corner. John wandered over and saw that it was none other than Dr Rodney McKay, Chief Science Officer and Pain In The Ass.

Sheppard knew he was being unfair to the Canadian – he'd not really known the man for all that long and had never been one to judge a book by its cover. Sure the scientist was rude, obnoxious, arrogant, egotistical and loud-mouthed, but the pilot had a feeling that there was a lot more to him than his outward appearance. McKay had already earned some serious Sheppard brownie points for showing him the Puddle Jumpers, so maybe he wasn't that bad. And the activating Ancient gizmos could be fun at times, especially the day before. He'd thought 'on' at a little blue sphere … which had promptly whizzed around the lab and smacked that idiot Kavanaugh right between the eyes. As soon as he saw how hard McKay was laughing, he knew that the man wasn't in the 'uptight and stuffy' contingent of scientists.

"Hey, Doc," he called, leaning against a workbench. "Whatcha doing?"

McKay looked up with an expression that could curdle milk and send children screaming to their parents, but it quickly transformed into a grin as he saw who the owner of the voice was. "Major!" he beamed happily. "Just the man I wanted to see."

"Oh, no way, McKay," John said, holding his hands up. "I'm not turning anything else on. Go and pester Beckett. Or one of the other dozen or so people with the gene." A sly grin crossed his face. "I'm not gonna let you pimp me out to your geeks anymore either, not without a cut of whatever they're paying you."

Rodney grimaced then shook his head. "Wonderful mental image there, thank you," he growled. "And who said anything about activation? I'll have you know, I don't need you anymore. You've been made officially redundant." His brilliant blue eyes twinkled with mischief. "And there's no severance pay either."

"What? Why?" asked Sheppard, suddenly feeling oddly put out.

"Because Carson's Highland voodoo works," McKay explained. "I am now the proud owner of one ATA gene."

"So how does it feel to be genetically superior?"

"How many times?! It is a random characteristic that…" Rodney trailed off as he saw the teasing smile on John's face. "Yes, very funny, Major."

"A riot," John agreed. "How do you know it works?"

McKay's face split into a crooked grin. "Actually, I need some help with that," he replied.

John shrugged. "Sure, I'm game. What do you want me to do?"

The Canadian grew serious. "Don't take this the wrong way, Major, but I want you to shoot me."

"WHAT?!" Sheppard was half convinced that he'd just completely misheard Rodney's request.

"Please, Major, I know what I'm doing."

"Obviously not, since you just asked me to put a bullet in you!"

"Do you trust me?" McKay asked suddenly.

"W-well, I, I…" John stammered, thrown by the sudden change of direction.

"It's a simple enough question!" Rodney snapped. "Do. You. Trust. Me?"

John thought for a moment and then nodded. "Yeah," he replied. "For some reason, I do."

"Good. Now shoot me."

John frowned, but pulled his 9 mm from his thigh holster. "Are you sure about this?" he asked, unconvinced. "It hurts a hell of a lot and the last thing Beckett needs is you cluttering up his shiny new infirmary and dripping blood everywhere..."


"Okay, okay." Sheppard sighed and brought the gun up to McKay's shoulder. "On three?"

Rodney steeled himself and nodded, closing his eyes. "Three it is."

"Okay. One."

John took a deep breath…


… and released the safety…


… then swung the gun down to Rodney's leg and fired.

There was a green flash that seemed to ripple across the Canadian's body, followed by a metallic sound as the bullet dropped to the floor. Green, John noted, not red. Blood wasn't green…

"What the hell?!"

McKay opened his eyes. "Hah!" he crowed. "I knew it would work!"

"McKay, I repeat, what the hell?!"

Rodney stepped forward, pointing to the oddly shaped device on his chest – and John almost kicked himself for not spotting it sooner. "Personal shield," the scientist explained. "I'm completely invulnerable!"

John meant to open his mouth to berate Rodney for not letting on sooner, for deciding to use a bullet as his first test, but when he did the only word that came out was, "Cool!" And he didn't care that he sounded like a ten year old boy at that point.

He still didn't care twenty minutes later after they'd tried a whole host of other things. As well as being bullet proof, they discovered that it was resistant to fire, water, electricity, baseball bats (which they'd borrowed from one of the botanists), fists and even walls.

"So what next?" asked John, grinning manically. He couldn't wait to have a go for himself and was surprised at how much fun McKay was proving to be. He'd been right earlier – he just needed to take the time to get to know the guy before judging him. The two of them had been trading barbs and insults for most of the time spent testing the shield and neither of them had given or taken offence – it had started to feel almost natural.

"I wonder…" Rodney began, then grinned evilly.


"How about a simple test of gravity?" He pointed in the direction of the Gate room. "We can use the balcony…"

"Hell yeah!" John agreed.

As they entered the Gate room and made their way up the stairs, John wondered if his geek choosing dilemma had been solved. McKay could well make a good addition to his team – he was certainly smart enough.

'I'll ask him after the meeting with Weir,' he thought, watching as the physicist prepared to be pushed over the railing. John grinned. Maybe it wasn't so bad in Pegasus after all. He quirked up an eyebrow at Rodney, who nodded.

"Okay, I'm ready!"