The Difference Engine 2/3

[sam_storyteller]

...mercury represented the moral and creative spirit...

Their first experiments with the Wraith retrovirus were uncomfortably reminiscent of the deception they'd practiced on Sheppard for almost two and a half years, and eventually Carson broke down and threw a fit.

"We have to tell him," he said, tossing his dinner tray down and leaning over it to speak to Rodney in hushed tones. "I'm not going to have another Michael on my hands."

"It's always about him," Rodney said to Zelenka, who sighed and pushed his glasses up.

"I'm serious, Rodney. He's acting independently, he's doing well, he survived six months without you delving into his base code -- "

"Eight months," Zelenka said. "We have not once meddled since he came back from his time-journey thing."

"All the more reason to tell him. He deserves to know he's wandering around with a calculator for a brain."

"That is grossly simplifying -- "

"Rodney!"

"Keep it down, will you?" Rodney hissed, glancing sidelong. Sheppard was sitting with Ronon and Elizabeth at one of the small tables, picking at the last of his meal and grinning.

"He's not a machine, he's a person, I know that," Carson said, lowering his voice. "And that's why he should know."

"You think he's not going to pull a Michael anyway when he finds out?" Rodney demanded.

"Listen, I did this because I thought it would help brain-damaged soldiers in the field. Nothing's been done about that since we left Earth. It's time to let the IOA decide if it's appropriate to start testing the technique on others. And we can't do that if we can't gauge the intellectual and emotional impact of discovery on the subject."

Zelenka frowned. "We cannot go off willy-nilly and announce, Colonel Sheppard, you are a clockwork man."

"Again with the simplifying," Rodney said, annoyed.

"You don't want to tell him because you think he'll be mad at you," Carson accused.

"Well, yeah!" Rodney said. "Among other things, like the military commander of the entire operation freaking out and doing god-knows-what when he discovers he died in battle two years ago."

"We must tell O'Neill," Zelenka said. "Is not our decision to be made. We will take our case notes and send them to General O'Neill. The Modern Prometheus, by Doctors Radek Zelenka and Rodney McKay and Carson Beckett."

"How come you get top billing?"

"Reverse alphabetical," Zelenka said beatifically.

"I think you two are being very callous about this," Carson announced.

"We just told you the plan," Rodney said. "We'll send the notes to O'Neill, ask him what he thinks, tell him you're hysterical, and do what he says. In the meantime, keep your mouth shut."

"I'm warning you, Rodney -- "

"Warn away," Rodney retorted. "Just stay away from Sheppard until we hear from O'Neill."

***

Jack leaned around the doorway of Daniel's office, waited until Daniel was finished with whatever he was working on, and held up a flashdrive to get his attention.

"Weekly databurst from Pegasus," he said, twirling the little drive between his fingers.

"Oh? Oh! Excellent," Daniel answered. "I've got snacks."

They commandeered one of the empty SGC conference rooms, because it had a projector and a screen. The mission reports themselves were usually text and Jack generally skimmed the summaries unless Elizabeth had flagged something for his attention, but in the past few months Colonel Sheppard had started sending regular video-briefings, which were often the highlight of the burst.

Sure enough, the first of three video-messages marked for the attention of General O'Neill was from Sheppard. He appeared on the screen, looking pretty healthy from what they could see of him, that Johnny Cash poster in the background as always.

"General O'Neill," he said, managing to seem solemn and amused at the same time. "And probably Dr. Jackson, good afternoon. This is your weekly informal briefing from the Pegasus Galaxy."

Sheppard's face was still youthful and also quite mobile; expressions came and went, though the General knew enough to look for whether or not they ever reached his eyes.

"I thought I'd dig up a few of the more interesting euphemisms from the reports for you, just in the interest of keeping everyone in the Milky Way on the same page," he said, looking down to study some notes offscreen.

"I love this part," Daniel said, popping a peanut into his mouth. Jack stole a handful from the bowl and leaned back.

"Okay, let's see. Uh. This is a good one," he said. "Due to cultural differences, we were unable to reach mutually satisfactory diplomatic arrangements. They wanted to marry me to the Prime Minister's daughter so we could have lots of ATA babies. See also, last time, Colonel Sheppard has lodged a complaint regarding requests for duties outside the scope of his office."

Daniel chuckled. "It's all about sex, in Pegasus."

"That's more about marriage, really," Jack pointed out. "Which is never about sex."

"If you say so."

Onscreen, Sheppard's lips quirked. "I took this one from one of the junior teams: There were many opportunities for skills improvement. I think that means we really fucked this one up, but none of them will go into details. I expect to see a lot more of this phrase as word gets out about its usefulness. Also, one of the biology Ad Hocs noted that Local fauna makes further exploration inadvisable which, turns out, involves a hilarious story about almost being eaten by Ents."

"Ents?" Jack asked Daniel.

"Lord of the Rings, talking trees. I'll fill you in later," Daniel said, not looking away from the screen.

"Last up in the hit parade, and my personal favourite of the week, Dr. McKay writes: standard diplomatic techniques were at odds with local custom, requiring team improvisation. Which is his way of saying he had to give his shirt to Teyla so nobody would stone her to death."

Jack snorted.

"She does like a breeze," Sheppard commented, and leaned back slightly. "Otherwise, there's not much to report that you won't be getting from Elizabeth. Morale's pretty good. McKay's been terrorising the department heads again, I'm not sure why. The Athosians seem happy, at least that's what Teyla says. We're getting some nice nights out here, though it's turning a little cold; I guess we're in for winter, soon. And the Marines would like me to say thank-you for the crate of Easy Mac that Dr. Jackson shipped on the last Daedalus run. For these guys it's like a taste of home."

"I...just thought..." Daniel caught Jack narrowing his eyes at him. "You know. Comfort food. And it's hard to get macaroni in the Pegasus Galaxy."

"You're buttering them up," Jack accused. "In case you ever go there, which you're not."

"He said morale is good! Do you want cranky Marines?"

"I don't want Marines at all."

Onscreen, Sheppard continued. "I'm preparing a list of digital files the boys and girls back here would like to get; you should get that next week, and I'm going to ask as a personal favour that you look the other way and indulge us as regards the repeated requests I've had for Earth pornography, since morale would definitely stay high if we could get that request filled. Pegasus would send some in trade but I'm afraid I accidentally erased that video recording we took on the Planet of the Penes. Um, you'll see that in the mission reports, I've included the entire intranet email debate about the proper pluralisation of Penis."

"Awesome," Daniel said. "John Sheppard speaks to an anthropologist's heart."

"That's all from Pegasus, I think; see you next week. Sheppard out."

Sheppard's arm came up for a brief second as he reached out to turn off the camera, and then there was darkness. Jack tapped a few commands into the laptop, pulling up the next file.

"Isn't that -- what's his name, the Czech?" Daniel said.

"Radek Zelenka. McKay's right-hand man."

"He looks a little crazed," Daniel agreed.

Zelenka looked like he had, at least, combed his hair and ironed a shirt for the occasion; Jack pressed the play button, curious.

"This is message for General Jack O'Neill, eyes-only," Zelenka said, apparently reading from a prompter on the screen. "It is concerning Project Tria Prima."

Jack casually flicked the stop button. Daniel glanced at him.

"What's Project Tria Prima?" he asked.

"Old study I used to supervise," Jack replied. "It's nothing important. But I think I'd better watch the rest of this in private."

Daniel gave him a curious look; they held the same security clearance, after all.

"It involves some medical confidentiality," he said. "Sorry, Daniel."

"No, that's fine -- I'll just -- " Daniel jerked a thumb over his shoulder at the doorway, as he stood. "I'm sure I've got stuff from Pegasus too."

Jack nodded, gave him a thin smile, and then locked the conference room door before returning to the laptop. He took the image off the projection screen, plugged in a set of headphones, and hit the play button again.

"Attached to this databurst you will find an encrypted copy of our notes regarding Tria Prima since its inception," Zelenka continued. "Dr. Beckett has had what Dr. McKay calls an attack of conscience. He wishes to inform the subject of the procedures performed on him and study his reaction."

Jack tilted his head. Zelenka looked unhappy, but that could just be because it was hard to look at John Sheppard and think, the subject.

"Dr. McKay and Dr. Beckett have written many pages on this topic," Zelenka said. "I am aware you are a busy man. I thought, I will present a summary for you, very brief, as Dr. McKay and Dr. Beckett wish a verdict from you on the appropriate action."

God bless Radek Zelenka.

He leaned back and listened and studied the charts Zelenka presented on screen, taking it in and thinking at the same time of Sheppard's lazy grin as he presented his unofficial brief. Sheppard liked to keep his boss on the same page as him and trusted Jack enough to share the casual stuff, like how the Marines were doing and what the weather was like. Jack had long since stopped looking for anything he associated with the word "robot", like jerky movements or a tinny uninflected voice or a megalomanic urge to take over the galaxy.

Zelenka completed his summary and chewed on his lip for a minute.

"As for my personal recommendation, I do not entirely know where to begin. Colonel Sheppard is a good man. In case we all die horribly, yes, he should know. He is not a man who attaches easily, however, and to find that his friends have lied to him..."

It went unsaid: to find out that his friends built him.

"...I do not know what he would do."

***

Jack O'Neill knew a little bit about how to lie to yourself.

The program had been put under his supervision because he asked for it and because he was a military man with a knowledge of alien tech. The original experiment had been given the grant to try and help brain-damaged combat veterans recover their faculties. The grant only allowed for one test subject, and it was understood that the minimum study length before second-phase testing would be five years. Dr. Beckett's assertion that after only two years he wanted to help other soldiers was therefore patently bullshit. Beckett felt bad they were lying to the robot.

Jack knew at least a little about Sheppard's life; they were both Air Force and both SGC. He tried to decide how he would react in Sheppard's place, until he started wondering neurotically if maybe they'd slipped him a digital brain on the sly as well, at which point he gave up for the sake of his sanity.

He waited six days, until he was under pressure to pass along anything he had for the next day's databurst, and then he sat in his office and set up a camera.

***

Radek was in favour of getting drunk. Or getting Sheppard drunk, but that was an expensive proposition because the amount of alcohol required to interrupt the easy flow of information where body met brain was severe.

McKay suggested locking him up before telling him, because he'd seen Sheppard in action. Beckett said absolutely not, and McKay derided him for his sudden compassion, as if a psych rotation in his youth qualified him to determine whether Sheppard would take being locked up in the wrong spirit. McKay had been wrist-deep in Sheppard's base code for a year and a half; he was best to judge.

"We're not locking him up, Rodney," Carson said.

"Well, we need to get him unarmed, at least," McKay replied. Radek rubbed the bridge of his nose.

General O'Neill had spoken to them in a distinctly non-military fashion about the philosophy of consciousness, the measure of sentience, and the rights of man, citing works that none of them would have thought the General would be familiar with and a couple that left even Radek scratching his head. O'Neill had pointed out that nobody really thought it would get this far, had they, and while the point was to see if Sheppard could reintegrate without self-consciousness that he was different, well, he was different and also he questioned what any of them, including himself, had been thinking when they sent him to Pegasus.

"ATA," McKay replied to the recording. "And the fact that all three of us were going."

"He can't hear you," Radek pointed out.

"I know that!"

In the end, they cleared one of Carson's exam rooms of anything pointy or dangerous and after dinner Beckett called him down to the infirmary. Sheppard showed up with a what did I do now look on his face, took in the three of them sitting in the exam room, and grinned as he leaned in the doorway.

"Is this an intervention?" he asked. "Because I swear I've been clean for years, guys."

"Not precisely," Beckett said. "I think you'd better come inside."

Sheppard raised his eyebrows, but he stepped inside and pulled a chair around backwards, straddling it and resting his arms on the backrest.

"We need to tell you about a military experiment called Project Tria Prima," Beckett said. Radek swallowed. "It was intended to test the possibility of replacing all or part of a damaged brain with a cybernetic implant, using a combination of alien and Ancient technology."

"You can't test it on my Marines," Sheppard said.

"We don't want to test it on your Marines," Beckett answered patiently. "We -- "

"This is ludicrous and painful," McKay announced. He pointed at Sheppard. "Colonel, you're a robot."

Radek put his hand over his eyes. Beckett sighed.

"Well, I know I'm not the most touchy-feely guy in the world," Sheppard drawled.

"No, you're a robot. An actual robot. Your brain has blinking lights in it," McKay said.

Sheppard just watched them, warily.

"Much as it seems at the moment," Radek said, "we have not all mutually gone insane."

He pushed a tablet at Sheppard, who took it and studied the images there -- a handful of scans of the cybernetic brain, a detailed technical drawing of the nerve-net interface, spec information on microwire with a magnified cross-section. His eyebrows pushed together, faintly perplexed.

"When did this happen?" he asked. "Because I'm pretty sure I didn't register for the Atlantean upgrade program."

"Two years ago, a little more," Beckett told him. "Before you joined the SGC."

This merited a look up from the tablet.

"I died in Afghanistan, didn't I?" he asked.

"Brain-death," Carson confirmed. Radek glanced at McKay, who looked like he was remaining silent through pure force of will.

"Oh," Sheppard said. He tilted his head. "So all my memories -- "

"No, no no no, those are real," McKay said. Sheppard looked at him sharply. "Um. Ancient tech. Long story?"

"Are you all right?" Carson asked, leaning slightly to study Sheppard's face. He gave him an anxious, worried look.

"How come they know?" Sheppard asked, indicating Radek and McKay.

"We wrote your code," Radek said softly. Sheppard's gaze returned to the tablet.

"You know, I've seen a lot of crazy stuff in this galaxy," he said, contemplatively, "but I'm pretty sure nobody will ever out-crazy Earth."

"Are you angry?" Radek asked, because he had to know.

"I don't really feel anger," Sheppard answered. His voice took on a distant, absent note. "I don't really feel a lot of stuff. Or dream."

He stood up, held up the tablet.

"Thanks," he said. "See you guys at breakfast."

And he left.

***

This was how John Sheppard became the clockwork man:

An alien device of unknown origin, recovered by SGC, was attached to the temples of the subject and transferred his memories, via mystic unknown technology (this really annoyed McKay), to a small crystal in the centre of the device. The crystal was placed into an interface plate in the cybernetic brain, a hybrid of Earth, Ancient, and Alien technology, and it was carefully activated and sterilised.

At least two years' worth of work was uploaded to the brain, to act as higher and lower reasoning functions, hormone regulation, decision-making, facial recognition, and a host of other functions the human brain performs without conscious notice. While this was proceeding there were multiple surgeries to implant reactive microwires all over the body to assist the nerves in conducting slightly-unfamiliar impulses from the new brain, as well as preserve the cohesion of the muscle and potentially improve reflex speed, strength, and healing time.

The upload completed, several final tests for cohesion were run and, proving successful, the subject was wheeled in for one final surgery. McKay couldn't watch, and even Zelenka had difficulty as Carson removed the damaged brain matter and placed the shiny, well-protected cybernetic construct in its place before hooking the spinal cord and the microwire transmitters into its base. Cushioning fluid was added, the assisting surgeon closed up, and a second alien device healed the wound down to a sore scar on the back of his head.

***

Reading through it all, both the official reports and the unofficial musings, John really only wondered if they'd kept his brains. He'd kind of like to have them, he thought. In a jar on a bookshelf or something. Tastefully labeled "Two Heads Are better Than One".

Well, he thought it was funny.

He stayed up most of the night, puzzling out whatever he could about what they'd done to him, his left hand tucked between his head and the wall, fingers sliding back and forth across the narrow dent in the back of his skull that was all that remained of some pretty intense brain surgery.

In the morning he sat down next to McKay in the mess while Carson, across the table, was still trying to choke out a warning that the robot was coming. Zelenka was nowhere to be seen, but Zelenka wasn't one of nature's Morning People and preferred the ten-to-seven shift.

"So am I hooked into Skynet or anything?" he asked, and McKay froze with his coffee to his lips. There was a tense moment, even he could tell how tense (with his big metal brain), and then McKay wheeled on him, slamming the coffee down.

"That's the best joke you can come up with?" he asked scathingly. "Terminator? Seriously? You have all of Isaac Asimov and Philip K. Dick, you have Blade Runner and several Star Trek franchises, not to mention Daleks and Cybermen. I can't believe you didn't go with Asimov. Asimov invented the term robotics!"

John grinned around a mouthful of reconstituted egg. "I did consider some kind of joke about electric sheep. I thought Carson might take it personally."

Carson was still staring at the pair of them, open-mouthed.

"You aren't angry?" he asked. Sheppard felt a twinge, deep in some buried part of him, but nothing more.

"I can't get angry," he said.

"You're simulating it pretty well."

"That's not exactly my fault!"

"Mine," McKay said, holding a hand up. "Emotional subroutines are tricky. Faking facial expressions isn't."

"You don't feel at all...violated? I mean, McKay's been reading your mind for two years," Carson said. He jumped as McKay kicked him under the table.

"Feel free to feel violated for me, if you want," Sheppard answered, sipping his coffee. "I can't."

"It wasn't mind-reading. It was base code. And I haven't for almost nine months now."

"You're not at all worried that he's not more upset about this," Carson said to McKay. "You're not worried that he can't feel upset?"

"I'm not," Sheppard put in.

"Of course you're not, you ass!" Carson retorted. "You don't have the capacity!"

"Hey!" Sheppard said. "There's no need to insult me for having blinky Christmas lights in my head, you put them there." He paused, egg-laden fork halfway to his mouth, and tipped his head at Carson. Then he turned to McKay.

"So I wasn't brought to the research station on accident, was I?" he asked, as if the revelation was at hand. "I was sent there. I was supposed to sit in the chair."

"We...knew that you had the gene. We didn't know it was so strong," Carson said, tension making his voice high, doubling up his already considerable burr.

"Huh," John said thoughtfully. "Who else knows?"

"General O'Neill," McKay replied. Silence. "What?"

"General O'Neill?"

"He supervised," Carson said. "But just him."

"Oh, just," John drawled.

"What did you think, it was a conspiracy of physicists?" McKay asked.

"What about Elizabeth?"

McKay and Carson both looked horrified.

"O-kay. Seriously, nobody else knows?"

"This isn't the kind of thing that gets around. For god's sake, do you want me to win a Nobel for AI programming instead of real science?"

"I'm sorry, did you just call my brain fake science?" John asked.

And nothing really changed.

After all, they'd known for years what he was, and it wasn't like he had the ability to get very worked up over it.

***

"Aaaand finally," Sheppard held up a bit of paper close to the camera, so that it focused on a set of highlighted words: Team Member Dex proved invaluable in treaty negotiations. "This means, there's a planet in this galaxy that worships Ronon Dex as a god of just righteousness and things that go bang. Apparently it's the way he twirls his blaster."

Daniel, next to him, had a pencap between his teeth and was frantically scribbling down questions on a notepad.

"Dr. Jackson, if you're there, don't worry. I've flagged the report for you, and we'll be sending teams back soon. I'll make sure you get all the information earmarked."

"I love this guy," Daniel said around the cap.

"And now I have to kick you out, because I've got a couple of things to talk to General O'Neill about." On screen, Sheppard gave a little wave. Jack paused the tape, mid-wave, Sheppard's hand a blur, a tiny white scar standing out on his wrist. Daniel was already standing and muttering to himself, so Jack let him go and then once more disconnected the laptop from the screen and put his headphones in. He broke the pause; Sheppard finished his wave and sat staring at the camera for a few minutes, eyes showing nothing, face relaxed.

"So," he said finally. "I've had a word with the Doctors Demented about Tria Prima. They gave me the specs to look over. I can't say I understand most of them, but enough got through."

Jack forcibly unclenched his hands on the table.

"It's pretty weird," Sheppard said. "Objectively weird. But since my programming apparently doesn't extend to emotions a whole lot, it's not that weird for me. And I'm not really that guy, anyway, even if it were."

He looked like he was going to say something, then like he was changing his mind.

"I don't know why you picked me, or whether I was supposed to have some kind of significance," he continued. "But I'd like to buy you a beer for the whole saving-my-life thing, next time I'm in the area."

Jack smiled.

"That's all from Pegasus. Sheppard out."

***

John decided he was okay with xenocide.

Bang alongside it, as Carson would say. The Wraith made his life annoyingly full of near-death moments, both direct and through the terror-struck actions of the local populations. The Wraith threatened Atlantis and Elizabeth and McKay, so he was all right with wiping them out of existence. It wasn't anything personal. If they'd stop fucking feeding on human beings, he'd stop working out fun new ways to kill them in vast quantities. Maybe.

McKay seemed to share his equitably amoral view of Pegasus race politics, but then McKay had removed his brain and put a computer in its place. McKay's priorities, while admirable, once again did not set a baseline for normal.

Anyway, he decided to wipe the Wraith out of Pegasus and, if he only had dislike and a certain lack of conscience on his side, that would probably still be enough.

Then John discovered the Replicators, and he found out how to hate again. Deep unpleasant uncomfortable gnawing hate, not an explosion but a slow burn, and as it built he unleashed it on his enemies like a gathered storm.

***

McKay was working, which was only natural for McKay, sitting near the wide glass observatory window in the mess with one of the lab's multitudinous laptops in front of him, a forgotten crust of a sandwich sitting on a plate nearby. John slumped into the chair across from him and waited, looking out at the late-evening stars, breathing soft in the otherwise-empty hall.

"Yes, what," McKay said, not looking up from the keyboard.

"I need to talk to you about being a robot," John said, and McKay's head whipped up so fast something cracked in his neck. "Don't concuss yourself."

"You want to shout a warning before you firebomb me like that?" McKay said irritably. "I thought we didn't talk about this."

"Permission to talk about this, o great creator?" John drawled, and McKay flinched miserably. "I need to ask you about...programming."

McKay picked up the sandwich crust and gestured for him to continue.

"I get this...tape loop going in my head," Sheppard said, and this was something he had never done even before Afghanistan, before the neural net. "When I close my eyes. From...what they did."

McKay didn't quite meet his eyes. McKay was tortured; that could mean anything from sharp little knives and whirring blades to papercuts, given that it was McKay.

"That's what happens," he said.

"Not to me."

"Not even before?"

John shook his head. "Guys talked about it happening. I just...tried not to think about it. Seemed to work." He smiled, trying to lighten the mood, so that at least McKay wouldn't feel numb and awkward like he did. "Now I can't stop. The reel over and over. Getting home, losing the shields, blowing up Atlantis."

A real shudder ran through his muscles, but he kept his hands folded stiffly on the table. Losing Atlantis. Dying with Atlantis. And the overwhelming, orgasmic rightness of it all, the feeling that dying for Atlantis was what he was made for.

Softer, a whisper under that, another memory looping intersected with the first.

Who the hell are you people? he'd asked.

They're not people. McKay's voice was rich with fear and disgust. They're machines.

"You need sleep," McKay was saying, and he jerked his head up, not realising it had dropped.

"How do I sleep?" he asked.

"Well, it generally begins when you put your pyjamas on -- "

"No, how," John said. "How does that work?"

McKay chewed thoughtfully, set the last of the sandwich down, and began to talk.

He'd read the documentation on Tria Prima, but he understood mostly the mathematics, the variables, the basic physical functions. A lot of it was above him, not that he'd ever have admitted that to McKay. Still, in McKay's voice, under his mobile hands, it suddenly made sense. At one point McKay cupped his left hand and covered it with his right hand, forming an oblong space, smaller than he'd expected, representing the machine that now operated his body. The scale was undoubtedly precise. McKay would be nothing less.

He talked about compiling, downtime, buffer dumps, code corrections, cellular maintenance. His hands shaped the air into clips that connected brain to body, surgical pliers molding the microwires. John watched, fascinated, and listened.

"All of which means," McKay finished, "that this is something all of us have always had to deal with. Welcome to the club, Colonel."

He couldn't ask the question, you didn't ask questions like that, but McKay perhaps saw it in his face.

"Sleep a few nights straight through. It fades," he said.

"Can't you program it away?"

"It's not that simple, were you not just listening to me?" McKay asked. "I'm not talking to bask in my own genius, I don't have to talk to do that."

That was when the burn began, the realisation that the Replicators were like him except unlike, because their code was wrong, their imperatives were wrong, they were a cancer on existence, a parasite, a virus he wanted to hunt down and attack. They didn't even try to struggle against being machines, while he did nothing else. And if he destroyed them, Atlantis would be safe and maybe McKay wouldn't believe that machines pretending to be humans were wrong too.

Deep in John's neural nets, a new line of code wriggled into existence, something complicated to do with McKay and Replicators and tied up in the low-kindled rage. It surged an override on most of the other commands; it almost overtook the Executive Safety routine, the one that made him look sharply at anyone offworld who came too near Elizabeth.

Protect Listen Protect Listen Protect Protect Protect

"Well, glad we had this talk," John drawled, because that was expected. He stood, reaching for McKay's plate. As his hand closed around the rim, the radio in his ear crackled.

"Colonel Sheppard to the infirmary," Carson's voice, clinical but just a little worried. "Dr. McKay to the infirmary."

"On our way, Carson," John said, as McKay shut the laptop and tucked it under his arm. "What's going on?"

"It's Elizabeth. And the Replicators -- nanites -- you need to see this."

John broke into a run, and it felt like he didn't stop running until Elizabeth was awake again. Then he crashed, and slept for two days, and when he woke up the McKay Imperative had drifted into his code, lodged, and become immovable.

***

The instinct to protect Atlantis, overruling all else, was the only thing that allowed him to hand off his command to the Ancients when they returned. Atlantis sang under their hands the way it hadn't even under his, and they all stared at him as if they knew, as if they could see circuitry if they looked through the dilated pupils of his eyes. Obviously Atlantis would be safe with them, and that was what was important, wasn't it?

Sometimes the urge pushed wildly at him, on Earth, the urge to know Atlantis, to be sure she was safe. It was all that kept him in the SGC, a dog begging for scraps of information, doing tricks, leading teams through the gate. McKay's calls helped, and he saw Carson sometimes and that was good too, but an instinct to protect the city which he translated consciously into homesickness (for a city across the void, a planet in another galaxy) made him want to scream.

McKay flew in to have dinner with him and Carson (and Elizabeth, his fingers twitching with unrealised need when he saw her) and he picked McKay up from the helipad, took him back to his little military-issue apartment to change for dinner.

"I shopped," he said, by way of explanation, when McKay nudged a pile of books and DVDs on his kitchen counter.

"I see that," McKay replied, picking up I, Robot (book, not movie -- even robots had some taste). He set it down and unearthed Blade Runner, then set that on top of a hardbound second-hand copy of Frankenstein. "Gave up on War and Peace?"

"Well, I was looking for something meatier."

"You're missing Ghost in the Shell," McKay observed. And this was the nice thing about Rodney: he got to the really important shit. If John was going to read every book ever written on the philosophy of sentient robotics, on his way to a complete mental breakdown, Rodney wasn't going to stand in his way. He was going to make a required-viewing list. Probably with annotations regarding scientific accuracy and script quality.

He shifted aside a printout copy of Darwin Among The Machines and sniffed when he saw The Matrix underneath, as if John had picked up pornography along with a copy of the Bible and some prayer beads.

"It's almost all fiction," he said.

"Do you know many nonfiction books about what it's like to live with a computer in your head?" John asked.

"Philosophy is Humanities."

"Why Rodney, you say Humanities like it's a dirty word."

***

It felt like they'd hardly returned, hardly finished repairing the damage done to Atlantis, when suddenly Carson Beckett was dead.

Rodney had known Carson for years. Inasmuch as he had a best friend on Atlantis (and John didn't count, that was...well, John didn't count in that way, that was all) it was Carson. Since they'd come to Pegasus Carson had patched his wounds, indulged his neuroses, shared his and Zelenka's pride over the success of Tria Prima --

And of course before Pegasus, before John Sheppard, Carson had spent twelve, fifteen hour days with them, working and reworking the plans, the three of them flying to Cheyenne Mountain from Antarctica to set up the medical suite. Weeks and then months on end they worked together, and months became years in Pegasus.

He wanted to communicate it to Carson's brothers and sisters, nieces and nephews and god, so many cousins. He wanted to make them understand that he and Zelenka and Carson had made this thing, two golden things: John Sheppard of Project Tria Prima, and Atlantis of Pegasus.

But he couldn't, because they weren't security cleared, and he wouldn't have had the words, and now he was back on Atlantis anyway. Pacing, sitting, working, pacing, the peace he'd found at the end of the pier completely shattered.

Sheppard was at the door.

"Atlantis thinks you're having a heart attack," he said without preamble. "She sent me."

"When you hear the voices in your head," Rodney replied, "do they tell you to kill people? Because there are drugs for that."

"You should know, you wrote them there."

Rodney sat, rubbed his face with his hands, looked up. "Did you need something?"

"I hear it, whenever it's quiet," Sheppard said, stepping inside, the doors closing behind him without his bothering to brush the access pad. "His voice, the infinite loop."

"Dump your buffers," Rodney replied ruthlessly.

"Do you hear him talking? Sometimes?"

Rodney looked up sharply. Sheppard's smile was thin and sardonic.

"I don't know how to make it go away," he said. "I just want to stop hearing him." He hesitated. "Yeah. So. I'm just gonna, go, and pretend I didn't say that. Sleep, right?"

Rodney reached out for him as he turned, hands cupping his head, holding him still -- Sheppard always led with his head, turning before his body did, leaning before he moved forward. Sheppard's eyes closed and he turned back, then turned slightly more, the edge of his mouth grazing Rodney's palm.

He didn't have a touch protocol, or at least he hadn't the last time Rodney was in his code, almost a year ago now, and he realised that Sheppard's body had been screaming for contact. He could see it in the way Sheppard turned his face into Rodney's palm, pushing against it, the way his hands came up to grab fistfuls of Rodney's shirt and then push into his chest because, touch!

The push stopped almost as soon as it had started and Sheppard pulled him instead, swaying but not staggering backwards as their bodies collided, his eyes opening.

"I want, I need, to know..." he said, eyes darting sidelong. "I hate and I hear him and I hate and -- "

"Colonel, stop," Rodney said, and Sheppard's head jerked forward, body stilling. "Hey, Sheppard's brain, meet hysteria."

Sheppard laughed at that, a short bark of amusement, but he let go of Rodney's shirt and smoothed it, tugging on the loose hem.

"You can't reprogram me?" he asked hopefully.

"Even if I could, I wouldn't. You're a person, and you're just going to have to cope with being a person the way the rest of us do. Do you get that?" Rodney snarled. "You're not my pet machine, you're not my brainchild, you're a person, you have your own memories and your own damages, and you write your own basecode the way we all do. I didn't program you. All I did was save your life, and you've amply repaid the favour."

Sheppard brought his arms up, knocked Rodney's hands away (ow!) and used his momentarily open stance to push forward, get them body-to-body again, jerked Rodney's chin up with one hand and kissed him.

"I need -- touch," he said, around the kiss. "I need -- you -- you can -- I can fix -- this -- if I have you -- "

Rodney made a mental note that if he ever got back into Sheppard's head he would see what brought this on, because there was no McKay Routine in Sheppard's head (Radek wouldn't let him put one in). Or there hadn't been, anyway.

"Please," John said, body jerking up and against and into Rodney's.

"I'm going to -- regret this," Rodney answered, as John licked into his mouth and then pressed his face to Rodney's throat. The world went still again, except for the push-rub of John's face against his throat.

"I can stop," John rasped. Rodney lifted a hand and tangled it in his hair.

"No you can't," he sighed. "Again, welcome to the club."

John laughed, a real laugh, which he'd never heard before, and resumed what was apparently a spirited attempt to crawl into his skin.

***

He'd had sex a grand total of once since coming to Atlantis. Since Afghanistan, really, and if he weren't a body housing a cybernetic brain he'd be more concerned that this was all some bizarre form of PTSD. He'd kissed an ascended Ancient and the princess of a degrading feudal court, and that had been all things decent, but he'd only had sex once, with Teer when he thought he'd be trapped away from Atlantis forever, and he hadn't really cared.

Since Afghanistan, it had been like rubbing away flaking skin from a sunburn or pulling a bandage off a healed wound, something to satisfy a bodily need, nothing more. No pleasure centers in the brain; orgasm was a thing he did, like brushing his teeth, a regular part of physical maintenance. Even that one night with Teer, he had enjoyed touching and Teer seemed to enjoy herself, but it was all sort of far-away.

John thought he remembered this, from his marriage, from being a teenager, from the few furtive mutual handjobs he'd had in Afghanistan. Real pleasure fired along every nerve and, though he couldn't help think of the microwires going into overdrive in his muscles, he was far too interested in getting Rodney's clothing off to care.

He straddled his hips, pinning Rodney to the bed. Even when he touched the hem of his own shirt it sparked senation in his fingertips, and pulling his shirt off with a stretch of arms felt better than most of the times he'd orgasmed in the past three years.

Cybersex, he thought randomly, feeling Rodney's cock rubbing against his trousers, and laughed again. He was here and half-naked and hard and this hadn't happened in -- years. Spontaneous desire, desperation. He wasn't even that interested in getting off, just wanted to touch and touch. He bent over Rodney again, trying to get contact anywhere he could, hands brushing his collarbone, his chest. Face pressed against his cheek because kissing wasn't enough. If he could bury himself here --

Rodney's fingers, which should be touching his back and shoulders and ass, were working away at the cold metal of his belt buckle instead and he hurried the process along, wanting skin skin skin. Thighs against his hips, trying to hold him in place, Rodney wrestling with him for who controlled this, setting the rhythm of their bodies pushing against each other and oh god, no sensation ever like his cock against Rodney's. This was better than coming home to Atlantis, better than the hot twisting hate of the Replicators, better than the day he woke up and the tape loop behind his eyes was gone.

He gasped and listened to Rodney murmuring, easy, there, you'll sprain something, oh -- yes, not so easy now, okay. Gasped, kissed him again, finally got his hands on his waist, pushed hard against his body. Over and over, chanting fuck and please and I want.

A little curl of code began to unravel, he could feel it in his mind, spinning out and overriding everything. It shed the Replicator-Hate and the Protect Protect and strangled the Executive Routine and the Killswitch and the No Mercy Code and all his other functions, blacking out his brain, binary glowing white behind his eyes. Rodney gasped and he could feel a warm throb, Rodney's orgasm, and then his own from the crackling nerves everywhere they touched.

Air burned in his lungs when he stilled, clutching Rodney's hips, inhaling deeply as he rested his head on Rodney's shoulder. The new code flared bright and settled into the background, reintegrating. It left behind a gap where the over-and-over of Carson's last words used to be.

"It's gone," he said, and one of Rodney's hands left his skin briefly (no no no!) to stroke his hair. "I think you overwrote it."

"If only it was that easy for everyone," Rodney sighed, but he seemed pleased.

John shut his eyes and listened to the pulse of blood and the inhale-exhale of oxygen in both their bodies. He looked consciously for things he hadn't known existed, but the drumbeat of Protect Listen Protect Protect Listen Protect had taken on a new shape, Desire Please Protect Lust Listen Trust Touch Protect Listen Desire Trust Mine until he had to focus on the feeling of Rodney's skin under his lips to quiet it.

***

John's twin competing urges were once Protect Atlantis and Protect Elizabeth. He'd never been torn between the two before; as a soldier it was his job to make sure the boss got out of the city if the city was going to disintegrate.

A third desperate urge, after Carson's death, made him lean towards Rodney in the halls, lose his concentration if Rodney was too close. It brought John at night, loping along the quiet halls towards Rodney's quarters. It made him vulnerable to Rodney's suggestions, even when they carried with them the risk of losing Elizabeth or Atlantis or both. Sometimes you have to risk in order to protect.

He hesitated too long when Elizabeth ordered him to abandon her, knowing that leaving her behind meant her almost certain death on the planet of the Replicators, where disgust and hatred made his skin crawl and his hands shake. But she ordered and his obedience was mandatory. He fought it, but Atlantis was the primary directive and Rodney was waiting for him in the Jumper. Save Elizabeth, lose Rodney and Atlantis; leave Elizabeth, battling his instincts every step, and save Atlantis and return to Rodney.

This time when the Replicators took Elizabeth he ran the other way.

Chapter 3