NOTES: This story came from out of the blue, though I suppose its inspiration stems from my disappointment with season two. I don't actually think McKay would do this, but it's what my muses demanded of me. Some readers may find some aspects offensive, so if you don't like harsh views of your favorite characters, please turn back now.

SPOILERS: through season two of Atlantis and season nine of SG-1

DISCLAIMER: Stargate: Atlantis, Stargate SG-1 and all things associated with it belong to other people.

RATING: K+

AMNESTY

Normally, when McKay was visiting the SGC, Sam could expect the pompous Canadian to pester her at least three times a day, hoping to regale her with tales of his discoveries and heroics in the Pegasus galaxy or pick her brain about some scientific issue only she was deemed smart enough to discuss with him. But this time, she hadn't heard from him once. While odd, the peace was not unwelcome. Then, on the day the Daedalus was scheduled to return to Atlantis, Dr. Weir dropped by Sam's lab to ask if she'd seen him. When she said she hadn't, Dr. Weir's expression grew worried, so Sam offered to help look for him.

She found the astrophysicist in the meeting room attached to the General's office. He was standing in the dark, in a corner, gazing through the windows at the Stargate in the Gateroom below. Shoulders hunched and arms wrapped protectively around himself, his stance reeked of fatigue and misery. On some level, it disturbed her. Although she'd seen the rambling, revealing message he'd sent to Earth when he'd thought he was going to die, she preferred to not have to think there was more to him than his snark and ego. Flicking on the lights caused him straighten, but he didn't turn to face her.

"McKay, what's wrong?"

He gave her a quick, surprised glance followed by a derisive snort. "You say that almost as if you care."

She walked up to stand next to him. "Let's pretend for a minute I do."

That got him to look at her. Sticking out a finger like a curious child, he poked her arm, a strange uncertainty in his eyes.

"What was that for?" she snapped.

"Oh," he said nervously, snatching back his hand. "N...nothing."

"So why are you staring off into space when you should be shipping out to the Daedalus?"

Turning back to the glass, he said simply, "I don't want to go."

"What do you mean?"

"I," he used his hands to emphasize his words, "don't want to go back," and his vexation at having to repeat himself, "to Atlantis."

"Are you nuts?"

A sad smile tugged at his lips. "Seems like I'm the only one who isn't."

"I find that difficult to believe."

He shrugged with false modesty. "But it's true." His eyes lit on her with desperation behind his conceit. "What does that say, when I'm the sanest person in the nuthouse?"

Unease stirred in her gut. "I don't get it, McKay. I saw your message; you said they were like family. How could you think about not going back?"

"That was before..." His gaze returned to the window.

"Before what?"

"Before everything went sideways."

"Sideways? What are you talking about?"

"I thought I had everything I wanted." He paused to give her a half leer, half smile. "Well...almost everything."

"I'm happy for you. Your point?"

"I was in charge of exciting, groundbreaking work. I thought I had friends and respect. It was sometimes tough and desperate, but we all worked together to get the job done." He began pacing restlessly, gesturing to add stress. "Then Everett's Marines arrived, then the Daedalus, then Ford got hooked on enzyme..." Pausing, a shudder ran through him, and he absently clasped his right elbow. From reading between the lines of the technical reports on Wraith ships, she could guess how close he'd come to joining the Lieutenant, a risk he'd apparently taken in a failed attempt to rescue his teammates. The cowardly McKay who'd first visited the SGC five years ago would never have dared such a thing.

"You don't want to go back because of what happened to Lieutenant Ford?"

Wagging a finger, he began pacing again. "Having someone you thought of as a friend take you hostage, drug you and shoot at you--that's just the tip of the iceberg. It's all been downhill since then." One hand swooped from his shoulder like a ski jumper. "I make one little mistake," he spaced a thumb and forefinger an inch apart, "and suddenly I'm a leper."

She knew he was probably referring to the Arcturus Project. "A man died, McKay, and you blew up most of a solar system."

"His name was Walter Collins, and you've blown up a solar system, too."

"It was a tactical necessity."

"And trying to control technology that might defeat the Wraith isn't?" He waved the thought aside. "So my arrogant attempt put Colonel Sheppard's life at risk. This is the man whose harebrained schemes have put my life and the lives of countless others in jeopardy time and again, yet I've stuck with him. But when my plan goes wrong, it's an unforgivable sin. Then Carson pulls a Dr. Mengela on me. I might expect that sort of thing from a military doctor under orders, but it was his idea! I would never have guessed that beneath that mama's boy facade was a rabid racial supremacist."

"Wait...how do you figure that?" Sam had met the Scottish geneticist; he'd seemed nice enough.

"He acts like being a Wraith is a disease, a deviation from humanity. They're their own species, for God's sake. Who cares if they evolved from the accidental mixing of human and bug DNA? They evolved. Thinking that they need to be cured of their Wraithness smacks of the same ideological bent as the Nazis attempting to create an Aryan nation. If you think about it too long, it's even worse. I can't believe he experimented on one..."

"People change," she offered. "You've changed."

"There's change, and then there's radical alterations to your core personality and values. It's almost like...they're not themselves anymore."

"You suspect an outside influence?"

The look he gave her was wide-eyed and shocked, as though she'd just spouted the unified theory. Suddenly he seemed elated, as though everything made sense. After a moment's consideration, his excited expression collapsed, and he shook his head. "No...I suppose not." He wearily ran both hands through his hair. "They were going to torture a man, Samantha, torture him based on the flimsiest of evidence--which proved to be baseless, by the way. Not that a lack of evidence is what really matters. Not that the incomparable idiocy of believing twenty minutes of torture will get you what you want really matters." Again he rubbed his right arm, this time below the elbow. "Or the illogic of choosing, as your torturer, a man whose only qualification is that he's an intimidating hulk skilled in killing Wraith. What made the whole thing completely insane was that she considered it in the first place--and that no one objected!"

"You could have objected."

He gave a dismissive flick of his wrist. "They'd stopped listening to me long before that point." Then he paused and nodded. "But you're right. I could have. I should have, though I didn't find out about it until after the fact. That I didn't say anything about it might be what bothers me the most. I just go along with it all. I'm a scientist, not a philosopher; I don't have a clue how to steer things back on course even if anyone would listen. She's supposed to be my moral compass...our moral compass. Did she think it would somehow be okay if someone who wasn't from Earth did her dirty work? Did she think, because the second guy she had tortured was the right one, it absolves her of any wrongdoing? Did she and Carson really believe they were justified in experimenting on a sentient being, forcing him to be human and lying to him simply because he's our enemy and wasn't human to begin with? Good God, we did worse to him than Hathor did to you on P8E-935! Is it that, because we're in another galaxy, we can abandon, in a year, all the principles we've spent centuries developing? She's not supposed to be a militaristic tyrant; she's supposed to be better than that."

"Militaristic? Thanks."

He rounded on her, all but pleading to be understood. "You know what I mean! Would General O'Neill have done what she did?"

Jack had been a POW and been tortured numerous times. He would never have done it.

"She's become a monster."

"Who's become a monster?"

Glancing behind him, Sam noticed Dr. Weir silhouetted in the doorway. Standing so close to him, she literally saw the color drain from McKay's face.

"Elizabeth..." He schooled his features and turned, chin up. "I ...I was just talking with Dr. Carter, here," he pointed at her needlessly, "about the trials and tribulations of running Atlantis." This was followed by a dry, awkward chuckle.

"We should've left ten minutes ago." There was a steely undertone to her mild censure. "Thank you for finding him, Colonel. How about you finish your conversation with a transmission from the Daedalus?" She turned, gesturing for him to follow.

McKay hesitated for a split second before dropping his chin and trailing after her like a submissive dog. Sam reached out, grabbing his arm and bringing him to a halt.

"Dr. Weir." The leader of Atlantis stopped and turned. "I'd prefer to continue our discussion. I think we're coming to a breakthrough." She added a smile and a bounce of enthusiasm she didn't feel. "It could be very important. Can't you just beam him up once the Daedalus is in orbit?"

With her face in shadow, there was no gauging Dr. Weir's expression. Tilting her head, she spoke with a hint of irritation. "If that's what you really want. We'll radio you when we're ready to break orbit." With that, she left.

Once Dr. Weir's steps grew faint, McKay's face fell into a grim smile. "Thanks for the effort, even if it only delays the inevitable."

"It doesn't have to."

He raised an eyebrow at her. "You say that as though I have an option."

"You're a civilian. If you want to leave Atlantis, you should be able to leave Atlantis. Others have."

"Others who didn't keep the city running. She won't take no for an answer." He gave a mirthless laugh. "And there's no hiding from Asgard beaming technology."

She felt her eyebrows crawl to her hairline. "Are you saying she'd abduct you?"

Throwing his hands in the air, he huffed. "These days, anything's possible. Besides, where on Earth could I go? What would I do? Return to the Russian naquadah generator program? Get tenure at MIT? There might be little for me to return to on Atlantis, but it's not as though I have anything here, either." He snorted in mock amusement. "I don't suppose the Asgard have an exchange program?"

Taking his shoulder, she turned him to the windows overlooking the Gateroom. "Who says you have to stay on Earth?"

His eyes lit up with the possibility. "But...how would that work? I'm not a part of the SGC..."

"Why don't we get you out of here, first, then figure out the details. SG-9 is scheduled to go offworld in..." She checked her watch. "About half an hour."

"It would cause you an awful headache."

The idea that he cared about it amused her. She gave him a big, self-satisfied grin and a reassuring slap on the shoulder. "What are they gonna do--fire me?"

That pulled up the corners of his lips. "But...why would you...?" He gestured between the 'gate and himself.

"During Anubis' attack, you helped me save Jack."

"And the world," he added, holding up a finger.

"And the world," she agreed with a smile. "Just returning the favor."

Pulling a few strings, Sam arranged for McKay to accompany SG-9 through the Stargate. The irony of sending him along with the primary diplomatic team was not lost on her. From there, he joined Colson's research group at the Beta Site. Then she contacted Dr. Weir while simultaneously sending encoded personal messages to various people on the Daedalus to whom McKay had felt the need to explain himself. Dr. Weir was not happy. Chief Harriman later confirmed that the SGC had been scanned by the Daedalus, but with McKay off world, the leader of Atlantis had been forced to leave empty-handed. They also discovered, during a routine inspection for Goa'uld, a tiny, semi-organic transponder had been implanted into the back of McKay's neck without his knowledge. Once removed, the device was revealed to be a hybrid of Wraith and human technologies--the development of which McKay, as Atlantis' Chief of Science, had never been informed.

While McKay's defection may have infuriated Dr. Weir, it didn't thrill Jack, either, but once Sam had explained everything, he started an investigation into the incidents McKay had mentioned. Jack also persuaded General Hammond to send the recently promoted Colonel Davis on the next trip to Atlantis. She'd hated it when her own actions had been called into question by the Pentagon, but if the morally ambiguous Dr. Rodney McKay felt the need to leave due to ethical conflicts, she figured that was reason enough to give it the once over.

To many, in the midst of the devastating threats of the Wraith and the Ori, issues such as ethics seemed trivial compared to survival. But why survive if it meant abandoning the very qualities that made life worth living and separated you from your enemy? McKay had felt there was no higher authority he could trust to make the right decisions, but she was lucky enough to know people worthy of her faith.