Author's Note: Life has been crazy. My apologies for the lack of updates, but hopefully that changes.

For the first time since he'd returned to Atlantis, Rodney McKay was alone in his lab. Nearly ten minutes ago all of the other scientists had headed toward the commissary for lunch. Rodney had declined the invitation, telling them that he was going to continue with his work instead. His excuse was only halfway true, but they had believed it, as he knew they would. Lately, the times when Rodney wasn't catching up with his teammates, he was working. As happy as he was to be home, the subtle pressure bearing down on him to 'go back to normal' was too much to handle twenty-four/seven. Working provided an escape. Engrossed in his experiments, he barely noticed that he could now remember almost every bit of research he had done on Atlantis. With that came more memories – memories of missions, of invasions, of space battles, of happy conversations, but also of things better left forgotten. Rodney had yet to decide whether it was a good or bad thing, but he felt he should know.

But today, he closed his laptop and rolled away from the table, tucking the computer beneath his arm as he did so. After a quick peek around the hallway to make sure none of his fellow scientists were around, Rodney stepped out of the room and began a speedy walk away from the lab. There were questions he had that needed to be answered – and no one here seemed to be willing to do so. He brushed his hand against an Ancient panel and slipped quietly into a room. The door shut quickly behind him.

It was a small room that Rodney had discovered more than a year ago. 'Room' was a little too generous – it was more of a large closet than anything. A monitor, an Ancient console, and a chair from Rodney's quarters were all the room contained. With a grim smile, Rodney sat down and set his laptop down gently by his feet. He had used this place often, but he kept the location to himself. The only computer that had access to the entirety of the Ancient database was the computer in the control room – and this one. Rodney supposed it was a safety measure in case the first was destroyed or invaded (which would've been helpful back when Koyla started his invasion, Rodney thought bitterly, wishing he had discovered it sooner). Even the small thought of a Genii made his muscles tense and he slowly forced himself to relax, setting his fingers on the console. The room had allowed Rodney to work through a chaos in silence several times – and once again, he called on it to help him.

The more that he remembered about Atlantis, the more he realized that things were different. He knew his absence was not the cause. From experience, he knew that loss brought the expedition even closer together. But he had returned to a splintered Atlantis. Everyone seemed to branch away from each other, as if there was some contagion in the population. John was abnormally reclusive, Elizabeth dined alone nearly half the time, Kate was often too busy with appointments to see Rodney for anything other than work purposes, Aiden and Teyla spent a majority of their time on the mainland… Even Rodney, normally so oblivious to people's emotions, could tell that, beneath their struggle to carry on with their everyday lives and to welcome him back, things had changed. People were angry, depressed, resentful, horrified…and no one would speak of it. Rodney's curiosity had driven him here, the one place where he could access every file in existence on Atlantis in private, the one place he could find his answers.

Rodney started with mission reports. Summaries filled the screen, and a particular one caught his eye.

Mission ID: PQ20165-5
Mission Status: Failed
Comments: Rodney McKay still MIA. No further information obtained.

A knot formed in his throat as Rodney stared at the reports that filled the bottom of the page. Mission Status: Failedblinked vibrantly next to each one. Elizabeth had told him that they had looked everywhere for him, but now he could see the true scope of it. For a moment, he forgot his purpose, scrolling through the countless planets they'd searched, the favors they'd called in, the leads that went nowhere…

With a tight swallow, Rodney scrolled to the more recent reports, refocusing on what he had come here for. He read through the page and was surprised to find that, since the two reports that he guessed had occurred during the Wraith attack, there were only a few reports. Why weren't they exploring other planets? An apprehensive feeling trickled through him. Subconsciously steeling himself for what was to come, Rodney gazed at the reports from the siege.

Mission ID: PQ20165-7
Mission Status: Completed
Comments: ZPM acquired.

He paused for a moment. PQ20165 - he would recognize that number anywhere. He pushed away the sharp memory of his kidnapping, instead thinking of the ZPM the planet had on display. AR-1 had been negotiating for the ZPM, Rodney recalled. Had the negotiations succeeded after he left? Acquired. Something told him that Atlantis had tired of negotiations. Had the impending threat of the Wraith been enough for them to steal a ZPM? Rodney could imagine John's angry voice in the briefing room, exclaiming, 'They just use it for decoration! We're at war!' Rodney's eyes moved onward.

Mission ID: PQ00025-54
Mission Status: Completed
Comments: Natives hostile. Few refugees taken. ZPM acquired.

It took a while for his brain to digest it. The implications of the three lines of text sunk into his skin slowly, like a poison. He could try and pretend not to remember, but he knew all too well what planet PQ00025 was. The first time they arrived, they were having ritual human sacrifices of each person who reached the age of twenty-five. After that, they'd made several trips back. Rodney, Elizabeth, and Radek had been the most frequent visitors.

ZPM acquired. Rodney's heart pounded in his chest as if it was a crisis he could stop. The kids needed the ZPM for the shield. They were safe from the Wraith with it. Why had Atlantis taken it? Few refugees taken. Had they really been so desperate for ZPMs, for power that they would resort to this thievery? Natives hostile. The phrase repeated over and over in his mind. Two words made his blood run cold. He had seen that written on several summaries of missions he'd participated in. It meant bloodshed, death, guns, running for life… But they were just kids on PQ00025. There weapons weren't much more advanced than a slingshot. It was obvious who would have won a fight between the kids and the marines of Atlantis. But why would they fire on innocents?

The kids had tried to stop them.

Rodney could picture what happened now, the imagined scenes running through his mind. He thought of his two companions – he grimaced to call them friends – who accompanied him to the shield generator every time he visited. Were they here? Or had they been gunned down by a marine? There was just one line below the two entries before the summaries entered a pattern of treaty-negotiating and crop retrieval but little else.

Event Update: The Wraith vessels attacking Atlantis have been destroyed.

A loud burst of static and indecipherable speaking broke the silence. Startled, Rodney glanced around before realizing that he had left his radio earpiece on.

"What was that?" he questioned, too shocked by what he had discovered to sound as snappish as he had meant to.

"McKay, are you there?" it was definitely a girl's voice.

"Yes?" Rodney leaned back in his chair.

"It's Sora. I, uh…" she hesitated for a moment, and began again. "Whenever you've got a free moment, could you come and see me? I want to talk to you. I'll be in my quarters."

Rodney frowned at the odd request, but replied, "Alright." He glanced at the monitor briefly before standing up and picking up his laptop. If there was more to learn through snooping, he wasn't about to find out today. "I'm on my way," he said into the radio, and then turned it off. If there was an emergency, they could reach him in other ways. For now, he wasn't sure that he wanted to talk to anyone. He thought for a moment about radioing Sora and telling her that he was too busy, but the way that she had talked to him made it seem like there was something important she needed to tell him.

Maybe it had something to do with all of this, he thought grimly as he left.

"Sixty-Two."

Rodney looked up wearily at his name, bloodshot eyes glaring up at the two men entering his cell. "I have a name," he corrected them, his voice tight. It's going to take more than three weeks to break me, Rodney thought, hatred burning through every inch of his flesh, a canvas bright with the reminders of the brutality of these people. Still, he felt dread and hopelessness churning in his stomach wildly as he sat. He could do nothing but bear the wounds they gave him and resist.

"You are little more than nothing. You are a number, a means to an end." Their voices sounded hazy, like the words had traveled through water before they reached Rodney. Lines of dry blood ran from his ears down to his neck, a testament to the damage the two had dealt him the day before.

"A means to the end of Atlantis and the end of suffering for your people," Rodney mused, letting his head rest against the concrete wall. His captors stayed toward the other end of the cell for now, shadows covering their faces. "I'd say that's a lot more than nothing." He prepared himself for the blow to punish his insolence, but it never came.

"When will you break, Sixty-Two? I tire of this game," First interrupted. "Atlantis fights the Wraith as we speak. They have stopped searching for you. You are dead to them; dead to the world. Rodney McKay exists in their memories and you, Sixty-Two, will never exist anywhere but this cell."

"You didn't expect me to keep your little nickname once I'm free, did you?" This time the blow did come: a hard backhand into his already bruised cheek. Rodney spat the blood in his mouth and faced them again. He remembered sitting in a cell with John, silently panicking as John spat insults at their captors. But now more than ever he understood why John did it. They had to use the only tools they had available to fight back because not to fight was to lose; to lose everything.

"How is little Amaya these days?" Second questioned abruptly, glancing over at the cell that housed the sleeping child.

"I wouldn't know," Rodney replied evenly, his eyes locked onto Second's.

"But you guys are real buddies now, aren't you?" Second questioned. "We know you've been talking to each other, Sixty-Two." Rodney said nothing. Inwardly, his heart leapt against his rib cage for fear of what the monsters would do if they set their attentions to her. His worry was well-founded.

"Hit a sensitive spot, did we?" said First. "What's wrong? You look…worried," he continued, sneering.

Rodney was silent once more. It was one thing to rebel when the punishment would be dealt to him alone; it was quite another to do so when someone else had to pay the price. He watched Second pull a short metal rod from the belt at his waist, twisting the object in his hands while he spoke. Rodney touched the side of his jaw softly, knowing that the rod's shape was still imprinted in deep purple hues there from days ago.

"Do you know why she is here?"

"No," Rodney answered honestly. He knew that she had been wandering in a marketplace, having lost track of her mother, when she was kidnapped. He knew that she loved and missed her doll Tracy and he knew she was confused and scared. He knew that the fact she was even in this cell made him want to rip out the throat of every Genii he could lay his hands on.

"Her father was an enemy of Cowen's administration." It was a new voice this time, from out of the cell and beneath the dim, hanging lamps. Rodney's eyes shot to the outline of the man, nausea rising in his stomach. The voice was familiar – terribly familiar. The man stepped from the shadows into the light by the entrance to the cell and finally Rodney could see his face. "Hello, McKay."

"Kolya." Though his scraped and bruised hands protested, Rodney pushed against the ground and managed to stand, leaning against the wall slightly to support himself.

"I am glad to see you doing well," Kolya said with a smile as First opened the cell door. "I would hate for our time together to be short and painless."

"Yes, well, wouldn't that just be horrifying," Rodney answered numbly. The door slammed shut and he jumped at the loud, harsh noise. After a pause, he spoke again. "So you're the one behind this."

"I always liked you better than Sheppard," Kolya said, ignoring Rodney's statement. He clasped his hands behind his back and strolled back and forth in the cell. Rodney's eyes fell on the gun holstered at his hip. "You always knew the odds; knew how to reason. Sheppard…Sheppard would hold fast to his military training no matter what the stakes."

At the mention of John's name, Rodney felt a surge of emotion in him. Sheppard is. He was alive. The Wraith hadn't attacked yet. Or better yet, maybe they had. Maybe Atlantis had won without him. Maybe now they could devote time to search for him…

"I am about to appeal to your sense of reason, Dr. Rodney McKay." Kolya stopped his pacing and faced Rodney. "I have no use for this child," he gestured toward Amaya. "Her father was staging a rebellion against Cowen. He and his rebellion are dead now. I have two choices here. I can make her an example for others or I can send her back to her mother."

The nausea that Rodney had felt upon Kolya's arrival was now back in full force. First and Second had proven themselves adept at pain and misery, but Rodney knew Kolya's potential. His eyes couldn't leave the gun, remembering when its muzzle had been pointed to Elizabeth Weir, Kolya's finger closing on the trigger… He remembered the knife digging into his forearm, Kolya's voice but a whisper in his ear as he told Rodney all of the things that would happen to Elizabeth if Rodney didn't give in.

Kolya knew how to break people. Not for the first time in three weeks, Rodney was terrified.

"I want the code to your iris, McKay."

"I won't give you anything," he replied firmly, locking his jaw and closing his trembling hands.

"Because withholding information is such a strength of yours," Kolya said, his voice dripping with sarcasm, the emotionless smile curling around his lips again. His dark eyes met Rodney's. "I am about to give you a choice. Either you give me the code and I let her go home or…" he moved his gaze toward the other cell.

Panicked by Kolya's presence, Rodney hadn't noticed Second slipping outside of the cell. But now he watched the other man open Amaya's cell and step into it. He knew what Kolya was insinuating.

"No," the whisper left his lips without him even realizing it. Kolya took a few steps forward until he was within inches of Rodney.

"She is innocent, McKay. So very sweet…pure… But things will be done to her that make you prefer death over observance if you do not give me what I desire," Kolya placed his hand on Rodney's shoulder, digging his thumb into a bruise relentlessly. Rodney winced and let out a small groan of pain. "I will give her back unharmed to her mother. You have my word. I have no use for her. Just tell me the code."

"I can't," Rodney replied, horror thick in his throat. He felt every bruise, every cut, every scratch on his body. Was that what awaited Amaya?

"Look at her!" Kolya's hand roughly grabbed his face and turned it to the girl. She was laying in the corner, blonde hair fanned out around her face like a halo. Her face was settled peacefully in sleep, her body curled into a small ball. "Imagine what I could do. What I will do."

Rodney's heart thundered in his chest. "Don't do this, Kolya…"

"I must save my people, McKay. If you believe in yours, then they will have no trouble defeating me. Save her. Give me the code."

Amaya's eyes fluttered open. From yards away, Rodney could see the panic slowly settle in her eyes as she fully awoke and saw Second standing in her cell. The door slammed shut behind him.

"Fine. Fine! It's 2673 Alpha—"

Kolya backhanded Rodney, sending the other man spiraling to the ground. "You think I am stupid, McKay?" he sent his boot flying into Rodney's abdomen. "I know your panic code." He dragged Rodney to his feet by his tattered jacket. "Second!" he called to the other man.

Second's eyes went toward Kolya. Again, Rodney's eyes were drawn to the metal bar in the man's hands.

"No," Rodney squirmed against Kolya's grip. "No! There's another way… Don't do this…"

"Tell me the code, McKay, and I'll let her go."

"I can't… I can't…" the words were a faint whisper.

Kolya nodded to Second, who drew the bat back and advanced on the girl. She clambered back farther into the corner, bringing her hands up as if to defend herself.

"NO!" Rodney cried, throwing himself at Kolya. They hit the floor as Amaya's shrill scream lit the air.