When John woke up the next morning, the first thing he realized was that he had a horrible crick in his neck, most likely obtained from having spent the night in a chair beside Elizabeth's bed in the infirmary. The second thing he realized was that her green eyes were locked on his, watching him.

"H-hey," he stammered, sitting forward. "How are you doing?"

"All right…Are we in the infirmary?"

"Yeah. How much do you remember about last night?"

"I…I'm not sure."

"We were in your office, the power was out. I went to grab your arm and…I don't think you were in your office anymore after that point." Elizabeth closed her eyes.

"No," she agreed with him after a long moment.

"You want to tell me where you were?" There was another lengthy silence.

"I've made thousands of deals in my lifetime," she finally said. "With different cultures, different planets…it wasn't supposed to be any different. I shouldn't have gone alone. I wasn't even thinking about it at the time; I just had to do it…they were waiting for me, grabbed and blindfolded me. I think I was so afraid of what was going to happen to this city that I wasn't even afraid for myself. We needed their weapon; that was the only way we were going to survive the Wraith."

"You mean the Genii nuclear bombs?" Elizabeth slowly nodded, still not looking at him.

"You read the report; you know that I was taken to see a man named Prenum."

"Yeah, and I'm beginning to think a few things were left out of that report."

"I went with a deal to offer them; the C4 they had wanted in the first place in exchange for their weapon. They…they wanted more."

"What exactly did you promise?"

"Nothing but the original deal. I thought that they had agreed…but they wanted something else." John began to get some idea of where this was going; a feeling like ice water went down his spine.

" Elizabeth…"

"Prenum left the room, and I don't know how many others came in; four, maybe five…I still couldn't see anything. Th-they were so strong, there was nothing I could do but lay there while they…"

"Y-you don't have to say it," John told her, his voice barely more than a whisper.

Elizabeth finally looked up at him, her eyes displaying a vulnerability that most people never got to see. "I don't know how long it took, but after they were gone…I got up, got dressed, and walked out of the room."

"Why didn't you say something?"

"When? In between assembling nuclear bombs and watching you run off on a suicide mission?"

"I don't know, something!"

"Keeping us all alive was more important."

"Are you sure about that?"

"I was…After everything was over, after the city was safe…I just put it all out of my mind. I didn't think about it again until you…" John looked away.

"I'm sorry."

"It's not your fault, John."

"Maybe, maybe not. Maybe none of this would have come up if I hadn't…You know I didn't want to hurt you. I tried…I tried to get you to stay away."

"I know. It was my choice. Just like it was my choice to go to the Genii." They both looked up as the curtain around Elizabeth's bed was pulled back. Beckett smiled as he saw she was awake.

"How are you feeling?" he asked her.

"I'm fine, Carson."

"Mmm, well I think I should be the judge of that."

John got up from his seat, although he couldn't make his eyes meet Elizabeth's. "I'll come and check on you later," he promised her.

"Colonel?" she said before he could leave. "Don't do anything I wouldn't do." Anyone else would have thought that comment had to do with running the city in her absence, but John knew it was a warning not to go off half-cocked in getting retribution in her name. As much as he wanted to pound a few faces in at the moment – and he REALLY wanted to give out a few good pummelings – he wasn't going to say no to her.

"Deal," he agreed before leaving.

When a knock sounded on John's office door later in the day, he barely even heard it. "I've got reports from the power redistribution," Rodney told him, holding up the files. "I heard about…How's Elizabeth doing?"

"She'll be fine."

"Do you know what that was all about? Is she sick?"

"She'll be fine," John repeated, a little more forcefully. Rodney nodded.

"Of course. I was just…I'll let you get back to whatever you were doing."

"Rodney?" John finally said, just before he was out the door.

"Mmm?"

"I'm sure that the rumor mill is going in full force."

"What? No, no, of course not – "

"Rodney," he said with a knowing look.

"Okay, maybe a little. Everyone's just worried about her."

"I know. Just tell everybody that Eliz – Dr. Weir is going to be okay, and try to keep the really wild stories to a minimum." McKay nodded.

"Yeah, sure…And tell Elizabeth that the city's not the same without her up in the control room running it."

"Is it okay if we talk?" Kate Heightmeyer asked Elizabeth as she entered her little curtained off corner of the infirmary. She gave a slight nod. "How are you doing?"

"All right. Anxious to get out of here."

"I'm sure…I've heard you've been working a lot of hours recently."

"That's nothing new," Elizabeth told her. "I think the last time I got more than five hours of sleep, I was still teaching at Georgetown."

"You should take advantage of the fact that we have longer days here," Kate told her. "And I don't mean using the extra time to get more work done."

"I know. Colonel Sheppard is always on my case about that."

Kate smiled. "Have you been sleeping all right once you finally manage to get away from your office?"

"Mostly. I-I'm sure everyone on this base has nightmares. There are a lot of things in Pegasus we never imagined finding and not all of them are pleasant."

"What kinds of things are your nightmares about?" Elizabeth thought for a moment about how far exactly she was going to let this go.

"The Wraith…and other things. I…got a little roughed up while Colonel Sheppard was under the influence of the retrovirus. I know he'd never intentionally hurt me, and he feels horrible, but…"

"Even though it wasn't the 'real' him, it still looked like him, sounded like him."

"Yes."

"Did something happen last night that triggered your memories of what happened before?" Elizabeth slowly nodded, not wanting to have to lie out loud but unwilling to reveal anything else. It wasn't that she didn't trust Kate, but she'd never been the sort of person that had to talk about her problems in order to solve them. Telling John had been enough. "Are you afraid of him?" Dr. Heightmeyer asked.

"Not anymore."

TBC...

AN: I did the add-in from the Siege because I just felt like they got off way too easy with the Genii handing over their weapon. The Atlantis gang has really screwed with those people throughout season one. I respect Weir's powers of persuasion, but I don't think that talking would have cut it; the Genii's revenge has been foiled again and again. I felt the show kinda wimped out a bit in Siege2 (or didn't have enough time to do anything else.) Anyway, one of my roommates pretty much ordered me to develop one of the ideas that was floating around in my head, and this is the result. Thanks to everyone who's sent feedback so far; I really appreciate it. Keep it coming.