Note 1: Takes place some months after Ghost in the Machine

Rodney arrived in the briefing room, his eyes wide in terror. Beads of sweat adorned his pale face. He drew in short, panicked breaths.

"I am so screwed," Rodney whispered, his gaze locking with Sheppard's in a silent plea to make everything better.

"What's wrong?" Sheppard asked. He kept his voice level but his own adrenaline raced at the sight of his terrified friend.

Rodney began to pace all the while muttering about how very screwed he was. He stared, mouth half-open, glancing at the closed doors as if he could see through them to Woolsey's office.

"When did the Daedalus get here?" Rodney asked, his voice shaking.

"This morning. Caldwell is meeting with Woolsey now. Why? What's going on?"

"I am so screwed."

"You already said that. What you haven't said is why."

Rodney gulped much the way he did when someone aimed a gun at him. Only there was no gun-just Rodney in complete panic mode.

Sheppard drew a deep breath, searching his memory for anything that would explain Rodney's behavior. So far it had been a normal day except Rodney hadn't been around much. He'd shown up for breakfast happy enough until he'd checked his tablet at the table and his face paled. He'd left quickly, making an excuse about a meeting he'd forgotten about or something. He hadn't shown up for lunch. When Sheppard had radioed him to make sure everything was okay, Rodney had answered with a brusk "Go away" and "I'm busy."

Sheppard had figured he'd see Rodney at the afternoon briefing so he'd let it go. Now he wondered if that'd been a bad choice.

Rodney gulped again. "I didn't get the warning on time. I didn't know where the Daedalus was going and there wasn't time to do anything about it anyway. I thought I at least had time to break for it until I had a better plan but if the Daedalus is already here…"

Rodney allowed his sentence to drift as he once again gave a silent plea for help.

"You need to sit down, Rodney," Sheppard tried, motioning once again for the nearest chair.

"No, what I need to do is panic. Panic and pace. Pacing helps me think."

"Maybe so, but you're making me dizzy and you're not making any sense. Sit down." Sheppard added the latter in a firm voice—as an order.

McKay stopped. He glanced from Sheppard to the chair and then back again. At last he nodded. "Okay." He slid into the chair, cuddling his arms around his chest and laying his forehead on the wooden table. A brief whimper escaped followed by deep, purposeful breathing.

"Now," Sheppard continued, "tell me what's going on. Take it slow and start at the beginning."

If it were possible, McKay panicked more at the request. He shot out of his chair, waving his arms wildly. "I can't. Not to...I…I shouldn't have come here. I need to go."

"McKay!" Sheppard called after him as the doors slid open. Sheppard chased after him only to find Colonel Caldwell stood, blocking Rodney's path.

"Dr. McKay," Caldwell said calmly.

"Yes, uh, Colonel," Rodney said with a broken voice. If you'll just excuse me." Rodney tried to sidestep Caldwell but the Colonel moved into his path once more.

"We need to talk." Caldwell motioned toward the briefing room's door panels. His right hand grabbed hold of Rodney's left arm. Rodney did not flinch at the movement. On the contrary, he seemed to be expecting something of the sort.

"Sir?" Sheppard asked. "Do you mind—"

"Join us, Colonel," Caldwell said.

As Caldwell directed Rodney back into the briefing room, Rodney desperately tried to escape.

"I think my lab needs me. I just remembered that Zelenka was running his dangerous explosion experiment and I'd hate to—"

"Sit," Caldwell commanded, letting go of Rodney's arm and motioning toward a chair. Woolsey took the seat across from them as the conference doors slid shut.

"You realize, of course, the Daedalus discovered what you did," Woolsey said, taking his own seat across from Rodney.

At first, McKay opened his mouth to argue, but then he immediately nodded and slumped into the chair as though in defeat. "Obviously," he answered. "I received word this morning."

"Care to share with us how?" Caldwell interjected.

"I had fail safes in place."

"Of course you did," Woolsey answered. "Not entirely surprising, I suppose."

"Do you fully understand what you've done?" Caldwell asked. "I mean fully understand the danger you have put all of us in? This whole galaxy?"

"Please, we're not in danger.".

"You can't know that."

"Yes, I can. Smartest guy in two galaxies, remember?"

"For a genius you sure act stupid sometimes," Caldwell snapped. "You're going to help us fix this."

"No," McKay answered, chuckling slightly, "no, I'm not."

"What you have done," Woolsey interjected, "is inexcusable, reckless, and dangerous. It violates the trust of everyone here. You understand that, don't you?"

McKay didn't answer.

"Will someone please explain what the hell is going on here?" Sheppard demanded, barely keeping his voice level. "McKay?" he stared at his friend in silent conversation but McKay yielded nothing but resignation.

Woolsey nodded. "Perhaps it would be best to bring Colonel Sheppard up to speed before we proceed." Caldwell nodded. McKay trembled.

"We are here as a professional courtesy, Dr. McKay. As you can imagine, we have some investigations to complete before we can proceed. Daedalus scientists are combing your labs and computers for information as we speak. Colonel Caldwell and myself have some matters to check into and then we will return. Until then, I suggest you tell Colonel Sheppard everything before he has to hear it from us."

Colonel Caldwell straightened his uniform as he made for the door. "Colonel Sheppard?"

"Yes, Sir?"

"Just to be clear, Dr. McKay is to remain here until we return. Understood?"

"Yes, Sir," Sheppard responded, his stomach sinking.

As the doors slid shut, Sheppard rounded on McKay. "What the hell?"

Rodney responded by raising his chin in his trademark defiance before standing up and pacing some more. "I think Radek would make a good addition for your team. He's about as capable as I am and he's gotten used to off world missions. It's easier than choosing someone who's never been off world bef—"

"You're not getting replaced, Rodney. Now tell me. What did you do?"

"First of all, they're not going to let me stay on Atlantis. Not after I... Honestly, I'd be surprised if I avoid prison time." He paused a moment before standing up and waving his arms wildly, his eyes manic and wild. "Second of all, do you think the inmates in top-secret prisons are as rough as those in regular prisons?"

"Rodney?"

"I mean, I probably should have thought of that before. If I'd been smart, like really smart, like smart-me and not desperate-stupid-me. Which, by the way, is smarter than anyone else here on a good day. Except maybe you, because you are smart. And Ronon can be smart. Did you know that? In his own way that is. He knew we should have shot Michael back in the day and we probably should have listened."

"Rodney?"

"Anyway, if I'd been smart like I should have been then I would have gated to a far off world before they caught on."

"McKay?"

"Of course they were going to catch on eventually. I knew that. It was just a matter of time. But I couldn't see abandoning you and Teyla and Ronon or even Zelenka really without you all knowing where I went or what happened to me. Can you imagine me on my own trying to make it in Pegasus? Bad idea. Not that prison is that great of an idea either but I guess you do what you gotta do, right? I always knew there'd be consequences."

Sheppard blinked. He'd tried several times with a 'Rodney' here and there to interrupt the one-way conversation but none of it seemed to make a difference. Rodney was trapped in his own mind, fumbling through his nonsensical thoughts.

"McKay!" he shouted, his voice reverberating against the metallic walls. At last desperate blue eyes met his own. "Rodney," Sheppard added, softer, gentler. He made his way by his friend's side. "I can't help you if I don't know what is going on. Please."

Rodney's fell back into his chair, burrowing his head into his palms. "I saved Elizabeth," Rodney whispered. "I saved her," he repeated, although this time he sounded less resigned and more proud and resolute, maybe even surprised. He straightened. "I thought I'd gotten away with it, to be honest. Or maybe I just convinced myself even knowing they'd figure it out. Anyway, I saved her."

While Rodney retained his cool, Sheppard seemed to lose his. His heart paused. The walls closed in. His first attempt at breathing failed. The second didn't do much better. Sounds ceased for a moment before he forced the panic back. At last he managed, "You reactivated the replicators?"

"Yes. No. Sort of? They're not really replicators and it was just Elizabeth anyway."

"Damn it, McKay!" Echoes of the same words came back to him from all that time ago when they'd first lost her—when McKay disobeyed his orders and put the nanites in her system. He'd disobeyed Sheppard again when he refused to shut them down.

Sheppard's stomach tightened as he thought of Elizabeth adrift in space, a machine no longer really human and no longer really alive, but somehow full of honor and so very Elizabeth. Nightmares still plagued him from what they did to her-what he did to her. He knew she understood why. It was necessary.

Sheppard refocused his attention toward Rodney who was no longer shaking. Instead, he glared furiously. "I saved her," he reiterated, carefully and slowly enunciating each word. "I saved her and I don't regret it."

Now I have to save you, Sheppard thought, not daring to say the words aloud.

He shook his head, stuffing his hands in his pockets if only to keep them from punching his friend. The primal instinct surprised him.

Sheppard felt betrayed, he realized. Betrayed from all the times Rodney refused to listen to him and all the times he disobeyed Sheppard's orders. How many times did McKay have to play with fire before they all burned?

Anger flooded Sheppard as a million security threats passed through his thoughts. He found it difficult to escape but still managed one word. "How?"

"Remember when I was kidnapped a few months back."

"Which time?"

"The one with the Genii rebels. The last time with the Genii anyway. I think it was the last time. Maybe not? Either way, that faction that refused to listen to the government that they all claimed didn't exist any more?"

"Go on."

"Right. Uh…I didn't really escape on my own. In fact, I wasn't really kidnapped. I may have faked the whole thing to steal a jumper."

It took a moment for Rodney's fast mumblings to register. Sheppard opened his mouth to respond but no words came out. His gut tangled in knots. He clenched and unclenched his fists.

They'd searched for Rodney for several days. They'd feared the worst. Only Rodney returned on his own four nights later with no injuries and little memory of what had happened during his capture.

"Son of a—" Sheppard felt the anger radiate from him. He took a few steps back, desperate to keep it together.

"You faked getting kidnapped?" he asked, saying each word slowly and deliberately. Nails dug into his palm as his fist tightened.

"Yes," Rodney answered, taking a few steps back himself. "I know I—"

"You know what it is like every time we go out there and one of us doesn't come back. You know what we went through looking for Teyla!"

Sheppard realized he was yelling but the fury inside him boiled. He continued, "You know what we go through every time some idiot gets it in their mind they want your brain and decide to take you. You are aware of every moment of anger and..."

Sheppard paused, words catching in his throat. "Knowing all this, you faked your own kidnapping."

"I didn't have a lot of time to plan and I needed to act. It was the only way."

"Right. The only way to steal a jumper so you could rush off and rescue a replicator."

"Rescue Elizabeth. You know as well as I do that it was her. I don't care whether or not it was her idea, no one deserves the fate we gave her. After everything she did for us."

"It was dangerous and stupid, Rodney."

"Maybe, but I had to do it and you know it. If you didn't think I'd try to help her then you don't know me very well."

"Up until a few minutes ago, I didn't think you'd steal a jumper under my nose and fake your own kidnapping. So, yeah, maybe you're right. Maybe I don't know you."

Sheppard felt himself shake but couldn't steady himself. Adrenaline coursed through him, fueling his anger. He stared at his friend—his teammate—and took another step back. "Damn it, Rodney," he added when McKay gave himself no further defense.

"So as I said: I am so screwed," Rodney moaned, slipping back into his chair.

"You disobeyed my orders again. Just like when you first activated her. Just like when you refused to shut the nanites down."

"I know. I…I'm sorry. I know it doesn't make it better. I know you're pissed and with good reason but…I had to do this. It was my fault Elizabeth was there to begin with."

Silence surrounded the room. Sheppard embraced it, allowing the quiet to calm his fury. He heard Rodney's head thump softly against the wooden table. Air circulated the room from fans overhead. Sheppard focused on Atlantis's low hum.

At last, Sheppard allowed himself a final deep breath. His fists loosened. His heart steadied. He settled into the seat next to his friend.

"Tell me what happened so I can help you."

Rodney gulped then nodded.

"After I stole the jumper, I gated to the space gate where…where we spaced them. I got Elizabeth on the jumper. Her power levels were low and I needed them to stay that way until we were far from the others. I took her to a planet I read about in the ancient database a while back that I'd kept secret. It was another planet where they were experimenting with the replicator technology. I knew there would be power there for her and a way for her to make herself the human-form body."

Hope surfaced. Sheppard imagined Elizabeth's smile and felt her calm warmth. He hated leaving her behind but she'd insisted it was necessary. So often lately the greater good kept him from doing what was right.

Where everyone else failed Elizabeth, Rodney kept insisting on bringing her back. His heart could allow no other choice. For a moment, Sheppard envied him.

"So she's human again?" Sheppard asked at last.

"Yes. Sort of. Mostly? I checked the programming over and over again. She's flesh and blood now. She can't replicate. She can't communicate with other replicators nor they with her. She poses no threat to anyone. Who knows, she might even be capable of ascension."

"Where is she now?"

"I let her choose a place without telling me. I knew it was possible we'd learn about her either from an off world team or the Daedalus would discover her existence somehow."

"Which was the warning message you got this morning. It was from her?"

"It wasn't so much a message as a signal, but yes."

Dread filled Sheppard. He longed to hear from her. He imagined her alive and happy somewhere.

Knowing Rodney risked all to save her.

Knowing Sheppard dared not risk the universe for her.

She'd made the choice to be spaced for the greater good and yet it still felt wrong to leave her there. He still forced the nightmares back where she called out to him, reaching for his help.

"Okay."

"Okay?" Rodney asked.

"Okay."

"I'm sorry, I don't know what that means. It seems to me this is anything but okay. I knew what would happen when I did this. I knew it wouldn't be a secret I could keep forever. But to lose Atlantis? It's my home, John. It's my family."

"I know and it'll be okay. Trust me."

Rodney nodded. "Okay."

The silence entered again. It was creepy. Rodney didn't do silent.

"You mad?" Rodney asked at last.

"What do you think?"

"Yes?"

"Hell yes. I'm pissed, Rodney. Seriously pissed."

Rodney stared at the floor, nodding. "I am sorry I had to do that."

"I know."

"You do?"

"You couldn't in good conscience leave her there. You also couldn't tell me because you knew I might have ordered you not to help her. I get that."

Rodney made to respond but Sheppard cut him off. "It's not that I don't understand. It's that you keep doing it. You keep disobeying orders. You keep putting your heart ahead of everything else, no matter the cost. It's noble. I'll give you that. It's also reckless and dangerous."

"Elizabeth deserved better."

"Yes, she did." Guilt entwined itself around Sheppard, choking him. He didn't believe in leaving people behind. At least he never used to. Looking back, he wondered when he first began this descent into darkness.

"So yeah, Rodney, I'm furious, but we don't have time to worry about that right now. Right now, you're in trouble and you need my help."

John felt Rodney's relief. He noted the silent thank you as McKay's gaze turned from desperate to trusting.

"I will fix this," Sheppard promised.

It took a few good hours before Caldwell and Woolsey returned. Sheppard ordered trays of food to be brought to the briefing room which had become, for all intents and purposes, Rodney's cell. Even with a few hours to think, Sheppard wasn't sure how to play his cards.

He wondered briefly if that was the real reason Woolsey and Caldwell had left them there so long. They both knew how much Atlantis needed Rodney. Maybe they were secretly hoping Sheppard would figure out how to fix everything.

"Colonel," Caldwell said, motioning toward Sheppard. "Am I to assume that you are now up to speed?"

"Yes, Sir. I am."

"Good. Then you understand our problem."

"Yes, Sir. I do."

"I think it is time for Dr. McKay to explain to us his side of the story," Woolsey said.

McKay glanced up as if noticing their visitors for the first time. "Right. Of course."

It didn't take long for McKay to rehash the facts. He told them just as he'd told them to Sheppard.

"She was furious when I woke up her up," he said, chuckling lightly. "She said she couldn't be trusted and that this couldn't end well. I believed different. I knew we could finally make this right. In the end, we did."

"You mean you hope you did." Woolsey said.

Rodney didn't disagree.

"She said that if it was discovered she was still alive that I should make sure you know the following. She doesn't blame us for what had to happen. She still cares for us and thinks about us. She wanted you all to know that she is for all intents and purposes human now and cannot pose a threat."

"Then why didn't she return to Atlantis?" Caldwell asked.

"You know as well as I do, Sir," Sheppard interjected, "that she'd be placed under tight scrutiny. She'd have no life here."

Caldwell nodded, seemingly satisfied by the response.

"There's no way she can do us any harm," Rodney said.

"She knows about Atlantis, Doctor," Caldwell snapped back. "She has valuable intel about all of us and our technology. If you are right and she is really Dr. Weir and human then perhaps we're not in danger. However, are we willing to bet everything on that chance? Even knowing what the replicators can do?"

Sheppard answered before Rodney could. "The fact is, Colonel, we don't know where Dr. Weir actually is. Even if we wanted to find her, she wouldn't let us."

"So what you are saying," Woolsey said, "Is that there is nothing we can do, either way."

"Yes. All we can do is wait and see if something happens."

"So for now we have only to deal with the consequences." Woolsey turned toward Dr. McKay.

"You need me," Rodney said, his voice low and shaking.

"But do we? Do we need someone who believes themselves to be above the rules? Who has a history of putting this city and this galaxy in danger when he believes himself to be above everyone else?"

Adrenaline spiked. Sheppard felt the room close in on him once more as he watched the anger in both Caldwell and Woolsey's expressions. Sheppard wasn't the only one Rodney had betrayed with his actions.

"To be fair—" Sheppard started, desperate to find a way to help Rodney. Shit. They really were going to send Rodney home.

"To be fair?" Caldwell cut-in. "We have been more than fair to Dr. McKay over the years. I admit he has saved my life and the lives of many in this galaxy on several occasions. He has also, however, blown up three-quarters of a solar system and he is responsible for the Asurans taking Dr. Weir in the first place."

"So what? You think we'd be better off without him?" Sheppard asked, glad that Rodney had the sense to stay quiet and let Sheppard do the arguing. "You're wrong. Do you have any idea how many times Atlantis would have been destroyed if McKay hadn't been around?"

"I think we are all well aware of Dr. McKay's abilities," Woolsey said, placing his hand on Sheppard's shoulder and motioning him back to his seat. Sheppard hadn't even realized he'd been standing. He glared daggers at Caldwell. No one was taking McKay away. No one.

"Atlantis is better with McKay here. You know that and I know that."

"How long are we to ignore his behavior?" Caldwell asked, his voice more gentle but his expression still firm.

"There must be consequences," Woolsey said. "I think all of us can agree on that."

McKay tucked his arms defensively around his chest. "I—"

"I got this, McKay," Sheppard said, cutting off McKay's reply. McKay's habit of saying the wrong thing and the wrong time could not play out today. Not if he wanted to stay on Atlantis.

Sheppard continued, "Exactly what consequences are we talking here? I refuse to accept any proposal where McKay is removed from Atlantis."

"We agree," Woolsey replied. He glanced toward Caldwell before they both turned back to McKay. Sheppard realized they'd already decided long before this meeting what would happen. All of this was a charade-a power play to make McKay understand how far he'd pushed them.

"I believe I have a solution that everyone will find acceptable," Woolsey continued. "Dr. McKay, you are to be placed on a three month unpaid suspension. During this time you are not allowed to use a laptop or any technological device in the city. If there is an emergency, then your colleagues will handle it. Maybe it's time you understood that Atlantis can exist without you and you are not outside of the rules."

"Furthermore," Caldwell added, "the charges against Dr. McKay are serious. He should spend the three months in a holding cell."

Woosley whipped around, clearly not expecting the addition. "You didn't—"

"It seems only appropriate. You and I both know that if he is allowed to roam freely, he will find ways to work and our point will be nulled. Same if we left him in his quarters. If we chose to charge him officially, he would be back in prison on Earth for a much larger portion of time. Three months is the least we can do in this circumstance."

"With all do respect, Colonel, this is my command," Woolsey answered. "All punitive measures are finalized by me."

"Maybe so, but I'm not suggesting this to be the bad guy. On the contrary, I'm trying to help. The IOA and the military are going to expect more than a slap on the wrist. You want to keep Dr. McKay on Atlantis, you'll have to satisfy their concerns."

Woolsey paused, straightening his papers as he considered the suggestion. At last he answered, "Fair enough."

Sheppard imagined claustrophobic McKay in the holding cells. Watching McKay tremble, he knew McKay was thinking the same thing. Still the scientist said nothing. It was better than losing Atlantis. Much as Sheppard hated to admit it, Caldwell was right.

Sheppard planned for how to help McKay during the three months. Teyla and Ronon could do shifts. Maybe Zelenka and Miko would also help out. Several others would volunteer. McKay had enough friends on Atlantis-whether he realized it or not-who could help him weather the storm.

At last, Sheppard nodded in agreement. "Thank you, Sir," he said to Caldwell, knowing that Caldwell of a few years ago would have pushed for stronger punitive measures. Pegasus had a way of changing people, sometimes for the better.

Woolsey continued, "After the three month period is over, Dr. McKay will be reinstated as chief of science and research. However, if he continues to put this city and it's members in danger despite command decisions, I will recommend his expulsion from Atlantis."

"Understood," Sheppard responded, remembering the day his own commanding officer had charged him with insubordination and disobeying direct orders. Some days Sheppard wondered how his life had gone so right after it had gone so wrong.

"Very well," Woolsey said, gathering his files. "Colonel Sheppard, please escort Dr. McKay to his quarters for now. We will meet shortly to go over final arrangements."

McKay stood up, his shoulders straightened and the terror gone from his eyes. "Thank you," he said at last, nodding to all in the room.

Sheppard leaned toward McKay, offering a brief nudge and a sympathetic smile. "Don't worry, Buddy, I have your back."