A/N:Hey, guys! So, this is the first part of my remix of ami_ven's 'On The Run' series from over on AO3. Because FF doesn't have a series function, I've put each work as a chapter under the title of 'The Wayfarer's Army'. They can each be read without the others and you don't need to have the whole series for it to still be enjoyable; they're really just one shots.

If you haven't read ami_ven's series, then you should go and do that because it's amazing. This is just an expanded universe so the stories and pretty damn similar but I hope you like it anyway.

This work can be read on AO3.

Read on, enjoy and don't forget to tell me what you think!

After gating back to Earth, John is arrested, court-martialed and thrown in prison for the death of Colonel Sumner. Rodney, fighting against the unjust punishment, breaks Sheppard free. They return to Pegasus, fugitives of Earth and Atlantis, and try to figure out what their life is now, what they are to each other and how they will continue to fulfil their mission: protecting the people of the Pegasus galaxy from the Wraith, all while trying to remain hidden from the teams of Atlantis still exploring the galaxy and the enemies they've made along the way.

Until There Rings the Snapping of the Chain

Until there rings the snapping of the chain
We wander through the day
Until our freedom rights maintained
We Wayfarers walk the dreaded bay

Rodney didn't even think about it which, in hindsight, probably should have been his first clue because he always thinks, he thinks too much, everyone on Atlantis had told him that at least five times. But not today, not when he got that call.

They'd been back on Earth for almost a month now and Rodney had no intention of leaving, not without Sheppard. Elizabeth was in meeting after meeting trying to convince this new general, a man named West that Sheppard didn't deserve this, that it was all a misunderstanding.

Rodney's approach had been less… diplomatic. That is to say he'd stormed into the general's office and flat out accused him of having a vendetta against Sheppard and trying to seize military command of Atlantis. He managed to rant for a solid five minutes before he was forcibly removed but not without getting a giving a few black eyes.

Rodney was entirely convinced this whole thing, giving them the ZPM, saving Atlantis, sending that arsehole Everett, was all leading up to the moment when they stepped through the 'gate to Earth and were immediately surrounded by the ominous clicking of automatic weapons being loaded, hard-faced men and women in army greens with unrelenting spines and a disembodied voice from somewhere in the observation room declaring the court-martial order.

Elizabeth had remained calm as always, John had just looked resigned but Rodney had all but exploded. He shoved the soldier trying to cuff Sheppard out of the way and demanded to see whoever was in charge and shrugged off the major's restraining hand as he lashed out when they tried to come closer. Eventually, they pulled him away and he was thrown in a cell for seven hours (five of which he spent screaming and two he spent pacing) before West showed up to smirk arrogantly as he recited the charges against Sheppard over the top of Rodney's entirely truthful counterarguments.

The entire thing was a sham and they all knew it. The only formal proceedings were the sentencing. There was no reading of charges, no 'guilty not guilty', no chance to defend his actions. After two nights in a holding cell where he was refused visitors, Major John Sheppard was dragged in front of a military tribunal to be told in no uncertain terms that he would be spending a very long time in Leavenworth penitentiary.

Rodney had called every high-ranking military officer he could think of, General Hammond, General O'Neill, hell, he even tried the IOA and NID. No one had known this was coming and no one could do anything about it.

Rodney was on his third night without sleep and his sixth cup of coffee that day when his phone rang. He had been busy sending emails across the country to try and get someone, anyone, to talk to him about what was happening with Sheppard. He had left his tenth voicemail with a man named General Landry who was supposedly taking over the SGC in the coming months and had been present at their debriefing. He was the only one in the party who had looked even remotely appalled by what had happened to Sheppard and Rodney was hoping that once he took control of the Program, he would have enough sway to do something about John.

Rodney picked up the phone with a terse, "General, if you'll just talk to someone, I'm sure we can straighten this out. Major Sheppard was just doing what-"

"Rodney." McKay blinked, his breathless rant halted because that… that was not General Landry.

"Sam," he said, shocked. He and Colonel Carter were still not exactly friends (to be precise, he was still an arrogant, self-important arse and she still didn't get that he flirted with her more out of habit than actual attraction now) but she had seen the way he was coming apart trying to get Sheppard out of this and the disgust had turned to a grudging respect. That didn't mean she called him though.

"Rodney, it's Sheppard." Rodney's stress-tense muscles tightened even further, his back shooting straight.

"What happened?" he demanded.

"McKay, you need to calm down and not do anything that-"

"What. Happened?" There was silence on the other end of the line. He knew what he sounded like, his voice raw and choked with anger and worry. He wasn't even yelling. His words were harsh and quiet and all too telling.

"He was stabbed."

And that was the point where Rodney proceeded to stop thinking. He slammed the phone down, grabbed his laptop, his mobile and his keys and slammed the door behind him before continuing to not think until he was here, sitting in the back of a puddle jumper with Sheppard laying on one of the benches swathed in blankets and groggily blinking himself awake.

He was so dead.

…

When John started coming to, the first thing he noticed was the pleasantly numb sensation of really good painkillers. The second was the distinctly unpleasant numbness he associated with falling asleep on hard ground when on a mission. The last thing he remembered was a predatory grin and pain exploding in his side. He forced his eyes open and frowned at the disconcertingly familiar sight of the equipment nets from a 'jumper. His frown only grew deeper when he heard a faint meow. He turned his head and saw a small tabby cat sitting on top of a pile of crates and boxes, watching him.

"Why is there a cat?" he croaked. From the front of the 'jumper, he heard a crash and a yelp followed by a curse before his field of vision was filled with worried blue eyes and a cautious smile.

"You're awake, that's good, great even. Do you want some water? Your throat sounds pretty dry and, I mean, of course it would be, you've been asleep for a few days now and-"

"McKay," John interrupted. "What's going on?" He watched curiously as Rodney back up a few paces and squared his shoulders, tipping his chin up to look down on him as if he was all mighty. John was familiar with this stance. It was the one McKay used when he'd done something idiotic and wanted to play it off like it was pure genius and shame on you for thinking otherwise. This was going to be good.

"Well, you were stabbed."

"I got that."

"And that prison was a hole."

"Knew that too."

"So I may have, you know, kind of-"

"McKay."

"I broke you out of prison."

John just had to sit and digest that for a minute. Rodney McKay, the man who complained every time he stubbed a toe and always insisted on checking with Elizabeth before they took any kind of action, had just committed a federal crime.

"You broke me out of prison." McKay was fidgeting now, doing that weird thing with his thumb and forefinger he did when he was nervous, shifting his weight gently from foot to foot.

"You got shived! What was I supposed to do? Wait around until the next time they killed you? And that's assuming you lived long enough for them to try again! Honestly, those butchers wouldn't know diazepam from cortisone. It's a wonder it's not already infected. I couldn't just leave you there and you didn't deserve to be there anyway so I may have forged your transfer orders, kidnapped you, stolen the 'jumper, put a virus into the SGC computers to lock them out for a few hours and 'gated to the edge of the galaxy."

John wanted to say something to that, he wanted to say a lot of somethings to that, but all he could manage was, "but why is there a cat?"

Rodney blinked and turned to look at the tabby that had curled up on its perch to watch the proceedings with narrowed eyes.

"Because I don't know if we'll ever be back and I didn't want to leave Schrodinger behind again."

"Didn't Carter have a cat named Schrodinger?"

"Great minds think alike I guess."

John looked at Rodney who was absently stroking the cat with his brow furrowed, clearly a million miles away. McKay had just given up everything, his home, his job, his friends, to get John out of a bad situation and, from the looks of it, at no small cost. John could tell he was exhausted, see the bags around his eyes and pinched look to his features, but his attention was more drawn to the black bruise rimming one socket and the suspiciously hand-shaped bruises on his arms and forearms. Whatever Rodney had done to get him out, he had done it fighting and for the scientist, that was a big deal.

The two of them had become close in the last year, best friends really, and John would like to think that he'd have done the same but the truth is, he just wasn't sure he would be able to. He could fight to save someone, sure, but this was giving up everything he loved and he didn't know he was without the military.

Right now, he supposed, he was a fugitive, he was a man on the run. But he was on the run with Rodney and somehow, that made it seem a little more bearable.

"So, what's the plan?" John asked. Rodney blinked and looked back at him.

"We go home."

"And how do you plan on doing that?"

Rodney rolled his eyes and pointed at himself. "Genius, remember?" He shifted his finger to point out the cockpit window. John craned his neck around from his prone position to see out the windshield.

"Wow…" Blue-purple light streamed in and around the 'jumper, drifting gently overhead and lighting up the whole compartment. John thought it looked like being inside and aurora. "Is that…?"

"I stole the Daedalus' hyperdrive schematics when I was poking around in the computers. I found most of what I needed to jury-rig something in the bases storerooms but lifting a Mark II Naquadah generator took a bit more effort. I jumped to a few different planets to make sure Earth couldn't follow us before I set down to set the whole thing up and I can't believe you slept through the whole thing, I mean what's the point of genius if nobody's there to marvel at it?"

Sheppard could only shake his head and laugh. This man had built a hyperdrive engine out of spare parts from the base storeroom and built it with minimal tools on an alien planet while on his own caring for a wounded teammate.

"Genius."