Evelyn POV

"Weir," I sighed into my radio.

I hadn't reported what happened with John right away. I'd gone back to my quarters, taken a shower, and laid on my bed and stared at the ceiling for a while in my towel. I now sat on the edge of my bed, leaning over my knees as I worried about everything that had happened.

"Captain O'Neill, Evelyn, is everything all right?" she asked, worry sounding over the radio. "The marines at Colonel Sheppard's door reported they had to stun him while you made a quick get away."

"Yeah," I agreed. "Yeah that happened. He's.. he's slipping quicker than I thought. I don't think he...he wouldn't have hurt me. But.."

"You took precautions, I understand," she answered. "Are you sure you're okay?"

"Yeah," I confirmed, though not very convincingly. "I'm sorry, I should have reported back in sooner, but I needed some time to process and I figured the marines would have informed you on the situation.. they're required to."

"No, it's okay I understand. If you need to talk about it myself or Heightmeyer are always available," she told me.

"Thanks but that's not necessary," I told her. "I'm gonna get some sleep before my next shift."

"Alright, take care," she told me. "I'll keep you in the loop."

I sighed to myself as I sighed off the radio and put it on my bedside. I laid back and lifted my feet off the floor and onto the bed. Too lazy to tuck myself in I fell asleep on top of the unmade bed.

I was jolted awake by a loud knocking at my door. I rolled onto my back and swung my legs over the side of my bed, running my dry tongue across my furry feeling teeth. I looked at the clock. I'd been sleeping for a while. I decided on answering the door, rather than giving my guest permission to enter, worried it might be John again. But then, he had an armed escort usually and I'll bet now he was confined indefinitely to his quarters.

"Took you long enough," Rodney greeted indignantly. I let out a breath I didn't know I was holding, a heavy feeling I didn't know I had released itself from my chest.

"Rodney," I breathed and closed the distance between the two of us, wrapping my arms tightly around him. He stood awkwardly for a moment before hugging me back tightly, rubbing soft circles between my shoulder blades.

"Are you okay?" he asked.

"Yeah," I nodded. "I just, I'm glad to see a friendly face. How'd the mission go?"

I pulled back, stepped away from the door and let him inside. I waved the lights on and winced, shrinking back from it's harsh glare. He glanced around at the unkempt state of my bedroom.

"Did I wake you?" he asked.

"Yeah, sorry, Weir and I have been taking shifts checking up on John," I explained. "So I've been sleeping when I can, if I can. And I was never really good at sleeping anyway. If you remember."

"Oh, I remember alright," he replied. "The mission went terribly by the way, which is kind of why I'm here."

I moved over to my bed, pulling the blankets over one handed to make things a little neater and sat down. Rodney joined me and ran his hands over his face.

"We.. we failed. We lost two marines," he explained. "We found some eggs we just couldn't get close enough, even with the saline."

"I'm sorry.." I said, bobbing my knee. This wasn't good. This meant we were going to lose John. I wasn't ready for that. Things between us, they'd just started developing into something I wanted. Or at least I had before the irratus part of him tried to sexually assault me.

"I am too," he said. "I know how much he means to you."

"Does everyone?" I scoffed. "Weir.. she kind of implied he was special to me in some sort of way."

"She hinted at that, and that was why she wanted you here. Honestly, I'm kind of glad she did deny my request to have you join us, the thought of losing you… I understand way more now why you were so angry with me over the whole," he said and I cut him off.

"I know," I agreed. "Listen, there's not really anything going on between John and I."

"No?" McKay scoffed.

"No," I confirmed. "It's not a well kept secret that I care for him, and he probably cares about me too but nothing's happened, nothings happening."

"Can't really blame you, I've never found myself particularly attracted to Waiths or Wraith hybrids either," he joked and I laughed. I rested my head on his shoulder for a moment.

"What do we do now?" I asked.

"Honestly?" he said. "I don't know."

Rodney POV

"Where the hell is the General's daughter?" Caldwell demanded once everyone else had gathered.

I shrugged. She'd been awake when I'd left her, so I doubted she had slept through the security breach announcement and the orders to gather in the gateroom. She had mentioned visiting one of the sites she'd requested access to regarding her power project, maybe it was taking a while to get back?

"Captain O'Neill please respond," I heard Chuck say into his headpiece. There was radio silence. She would have responded, even if she was running late. "Captain O'Neill, this is control, please respond."

"Captain O'Neill, this is Colonel Caldwell, please respond," Caldwell tried. "Alright, we don't have time for this. We'll deal with O'Neill AWOL later."

"If that's what it turns out to be!" I interjected. "Something could have happened to her. She's never failed to respond to a radio call before.."

"If that's not what it is then it's imperative we locate Colonel Sheppard," Caldwell shut me down.

I went back into reconfiguring the city's tracking system to get a lock on Sheppard's transmitter and tried not to worry about what had happened to Evelyn. Worrying about her wouldn't help me find out what had happened to her.

"Okay, we've got a lock on him," I announced. Everyone's eyes trained on the large display showing Sheppard's blinking transmitter.

"That can't be him," Caldwell argued. "It's moving too fast."

"It's him," Ronon confirmed, sounding a little bitter.

"Allright, four teams. Surround him and close in. I want him stopped, and gentlemen use whatever level of force you deem necessary. Move out," Caldwell ordered and all the marines turned and marched away. I couldn't believe this.

"What if he has O'Neill?" I butted in. I was scandalised. They could kill her. If he has her and they use lethal force she could be dead. I should have made her come with me after I went to go see her. The power project could have waited.

"Especially if he has the General's daughter," Caldwell replied. Why did he always call her that? She was a captain in her own right, and had a doctorate. But he still always called her the 'General's Daughter'.

"You will only use such force as a last result," Weir interjected, making the troop pause and I sighed in relief, at least someone had their head screwed on correctly.

"That's not Sheppard anymore, ma'am," Caldwell tried to argue.

"You heard me," Weir told the marines firmly, ignoring Caldwell's protests.

With the marines out of the room and Ronon and Teyla close behind it left myself and Chuck to coordinate the teams, Weir and Caldwell overseeing. I hoped by some miracle Evelyn turned up unharmed.

After locking down the stargate I watched Sheppard's transponder blink from one side of the city to another. Caldwell leaned in, just as confused as I was.

"I thought you said he couldn't use the stargate," he said.

"I said I doubted he was lucid enough," I replied, shaking my head. Damn it Sheppard.

"Well, shut them down. He's not going to do it again," Caldwell ordered.

"Thus stranding your search teams," I argued.

Evelyn POV

I sighed as I walked through a relatively dark part of the city. I could barely do my checks right as I sketched out places to mount my generators now that Weir had approved of my scouted locations. I was so distracted by everything going on with John I couldn't do anything right. Thankfully at least I'd backed up my tablet before I'd left to sketch on location so it didn't matter that it was sitting on the bottom of the sea floor.

I was shaken from my thoughts when I heard the sound of machine gun fire nearby. I cursed under my breath. Of all days for my radio to be rattling around in multiple pieces in my pocket, it had to be today. Had to be now.

I jogged along the corridor I was in, looking to get to a vantage point where I could see what was going on but be covered enough no one would see me. Luckily I was always packing, so even though I didn't have my P90, I still had my side arm and a few knives.

I heard running footsteps approaching but before I was able to react I felt my body make contact with the floor. I let out an "ooft" as I felt the wind leave my lungs and I scrambled on the floor to stand again.

Managing to get out from under him, I quickly realised it was Colonel Sheppard who had crashed into me. I grappled with him, using his surprise at me being her to get the advantage and slammed him hard into the wall. I was shaking, I couldn't make the same mistake as last time. This wasn't my John anymore, this was a Wraith, a hostile threat. And I needed to do what was necessary.

My pulse hammered in my ears as I reached for my side arm. Sheppard gripped me tightly by the back of my tank top. This was it. I had to kill him. The team failed, there was no cure. Only a monster that had taken over Sheppard's body. John held me tight and flipped us round, pinning me to the wall he was just up against.

He stared me down, watching me like a predator. He was waiting for me, waiting for me to take the safety off my pistol and attempt to fire at him. I stood frozen, again. He wasn't attacking, was he holding back? Was there still some part of John holding back part of the monster? Did I still shoot? I thought I had to. I thought there was no other choice.

I heard two more sets of running footsteps, a little ways apart. John let out a growl and gripped me tighter. I realised then, there was a part of Wraith John that didn't want to kill me, and probably wasn't murdering me right now because he wanted something else.

John dropped to the ground before my eyes. Vaguely I remembered hearing the sound of stunner fire and I stared down in shock at the body. The first set of footsteps slowed to a halt beside me and the second wasn't far off.

"Are you alright?" Ronon asked and I stared down at John, making sure he wasn't going to spring up off the ground like a horror movie villain.

"Yeah," I gasped. "Yeah I'm okay."

"Ronon!" Teyla called and then skidded to a stop beside us. "Evelyn? No one could get a hold of you. We were worried Colonel Sheppard had taken you hostage."

"I think he was about to," I answered.

"Get the doctor down here. I have him," Ronon said into his radio.

I sighed and put my side arm away, leaning over my knees as I let my heart beat settle down. This was way different than any of my past active combat situations could have prepared me for. Maybe I wasn't cut out for the Pegasus life.

One of the marines escorted me to the gateroom so I could debrief and explain to Weir and Caldwell why I was apparently considered AWOL. I perched on one of the chairs, still reeling from what had happened while Rodney looked over at me concerned. He was being unusually quiet at Weir and Caldwell exchanged a look.

"Why didn't you respond to your radio calls?" Caldwell asked. I reached into my pocket and grabbed the pieces of my smashed radio. I placed them down on one of the control desks and wiped my hands off on my cargo pants.

"I was sketching on location for one of my generator mounts and dropped both my radio and tablet. The tablet is currently in the ocean somewhere and my radio hit the deck and broke into this mess," I explained. "I heard the gunfire and prepared to engage when Colonel Sheppard crashed into me."

"You mean to tell me we were able to take down that thing because he tripped over you?" Caldwell asked, looking annoyed.

"Afraid so," I shrugged. "But like, Ronon also shot him and he and Teyla pursued him into the position he was able to trip over me so.."

"Alright, Captain, you're dismissed without reprimand," Calwell told me. "As far as I'm concerned you weren't AWOL and so long as you're unharmed I'm happy."

"Are you alright?" Weir asked me and I nodded. "Alright, you're dismissed. You can go visit the infirmary if you'd like."

I nodded. I didn't really want to have much to do with John at the moment, but I felt a strange pull to go to him, make sure he was alright. I was having trouble separating Iratus John from regular John.

Rodney walked over and put an arm around my shoulders, rubbing my upper arm lightly as I sat there. Eventually I pushed myself up and the two of us walked to the infirmary.

Teyla, Ronon, Rodney and I waited off to the side and observed the nursing staff check on John while he was restrained to the bed with thick straps. Weir, Caldwell and Beckett were off to the other side discussing John's condition just within earshot.

"I've put him in a medically induced coma for now. I was afraid he might break through the restraints," Beckett explained, that did explain why he was still out.

"That's a good call, Doctor," Caldwell praised.

"So, what now?" Weir asked. I stared sadly down at my CO. His now entire lower half of his face was mutated, along with both arms, and both eyes last I'd seen.

"The retrovirus has wreaked havoc on his system, and it's taking over," Beckett explained. It might be about time we said our goodbyes.

"What does that mean?" Weir asked.

"It means if we don't find a way to stop the retrovirus in the next 24 horse, what is left of the John Sheppard we know will be gone," Beckett explained and I bit my lip. Rodney gripped my shoulder, giving it a comforting squeeze.

"I'm uh, I'm gonna go to the mess," Rodney said and I dropped my head down to stare at my lap.

"I think I'll join you," Teyla said and Ronon grunted in agreement.

"I'm gonna stay a bit longer," I said softly.

Rodney POV

I sat picking at my bowl of fruit salad and jello while Teyla sat quietly on the other side of the table. Ronon leaned against the railing, more silent than usual. A heavy silence sat over the top of us. Our leader, our friend of some time now could be dead tomorrow. Because, if like Beckett said, and it was irreversible by this time tomorrow, someone would have to kill him. Like some rabid dog to be put to sleep.

"You guys are up late," I heard Weir comment. I looked up and saw her wringing her hands. I would have expected Evelyn by now.

"Can't sleep either?" I greeted.

"Any progress?" Teyla asked.

"No," Weir answered. "He's still in a coma. At least he isn't in any pain."

"Is Evelyn still there?" I asked. She'd refused to come here with the rest of us. She should have been here, she can't sit alone at a time like this.

"She won't leave his side," Weir replied. She sighed. "And he didn't stop asking after her. Whenever I stopped by all he'd talk about was the visit they'd just had or asked about her next one...I always wondered if there was some attraction between the two of them, because of how they acted around one another. And how every time she was injured he'd spend all day by her side. He's different around her."

I soured. We'd spoken a lot about this the last few days. I looked up and saw Ronon and Teyla exchanging a glance. Oh, now what did they know that I didn't? I stuffed another spoonful in my mouth.

"Maybe it's her returning the favor," Ronon suggested. "He's kept her safe now she's keeping watch over him."

"You're probably right," Weir agreed. "It's a little sad, isn't it? They'll never get their moment in the sun."

"Maybe if I went alone, maybe.." Ronon started. He wanted to do something, I understood. I wanted to help my friend, but there wasn't anything any of us could do. It was too dangerous and we were all out of options.

"It's not open for discussion," Weir replied.

"I'm not good at standing still," Ronon explained. I felt bad for the guy. Like myself, when Ronon had a problem, he fixed it. Now he couldn't, he was at a loss.

"I understand," Weir replied. "Believe me, I appreciate how you feel. Look, we have closed down that section of the infirmary but if you feel the need to… what I mean to say is if you would like to have a private goodbye, you should probably do it soon."

"Are we really there?" I asked. I'd been pretty realistic about this, I knew it was coming but having Weir actually say it…

"I think we might be," she confirmed.

"Dr. Weir, I need to speak to you immediately," Beckett said over the radio.

"What is it?" she asked.

"Meet me in your office, I think I have an idea," he responded.

Evelyn POV

I perched off to the side in the waiting area as Beckett and his staff worked on bringing John out of his coma. I didn't exactly like the idea of John going into that cave, especially by himself, but trusted Beckett. If he said it would work and that we had a chance at getting John back, I had to hold onto hope.

"Go get some sleep kid," Beckett told me. "I promise I'll let you know as soon as we get back with the eggs."

"I don't care what time it is," I said. "I don't care what state he's in."

"I know," he told me and put a comforting hand on my upper arm. "Go rest."

Restlessly I threw myself around in my sheets, unable to settle into a deep sleep, or any kind of sleep at all. I was up like a shot as soon as my radio crackled to life and Beckett told me they'd made it back and things were a success.

I ran down the halls as fast as my legs would carry me. I wasn't going to lose him. The team had made it back okay. Beckett told me he was about to go and create an antidote but allowed me in to see him. I sat in the chair by his bedside as he lay, restrained and unconscious. I chewed the skin around my thumbnail. We were in the home stretch. I shouldn't feel this anxious.

I rested my head on my shoulder, knees up at my chest in the chair while I waited. For what I didn't know. For a result I guess, a magic overnight change. But the reality was that wouldn't happen. We'd be lucky if Beckett's cure stopped him from being purple.

"It's not going to happen overnight, you can bet on that, but the transformation has begun to reverse itself," I heard Beckett say. I must have finally drifted off.

"So eventually he'sll be back in uniform," Caldwell stated.

"Eventually," Beckett agreed.

"Well done, Carson, for once again elevating medicine to actual science," McKay said, giving the Dr a backhanded compliment.

"Well, thank you, Rondey," Beckett said, taking it in stride.

I wanted to sit up and banter a little but, but besides listening, I couldn't really do much. The adrenalin of the whole citation must be finally wearing off. My body needed rest after the week we'd had. First the Ellia thing, the overnight flight back to Atlantis and then the four day saga with John. It was good he was back on the mend.

"You'll all finally be able to get some sleep, like Evelyn here," Weir commented. "Keep me posted."

"All right," Beckett agreed.

"We might uh," Ronon started.

"Stay a while," Teyla agreed.

"If that's okay," Rodney said and I smiled to myself in my half conscious state.

"Of course," Beckett told them warmly.

With John now on the mend properly, and Beckett seeing fit to bring John back out of the induced coma, I found myself keeping my distance from the infirmary. Now I wasn't worried about his life hanging in the balance, I was back to being confused about him. Especially after what Iratus John had been like.

I wasn't sure I wanted a relationship with my CO before all this crap happened, now it was only more complicated. I knew the almost assault wasn't him, it was the Iratus going after what it wanted. It was animal instincts, feed, defend and multiply. And I filled that last category. But it didn't make me feel any better. Knowing why Iratus John had down what he did, or almost did, didn't take away what had happened. It didn't make it any easier to separate the beast occupying his body from the kind, gentle and sweet guy I knew.

And so I kept my distance. It wasn't far to go to say I was avoiding him completely. I was practically cursing myself a week later when he'd been cleared to leave the infirmary and had walked into the gym when I was there. I'd hung back a little after sparing with Ronon to catch my breath and do some cool down stretches. I shook my head, I should have done this in my own quarters.

"Hey," he said softly.

"Feeling better?" I asked. "I guess you must be, if Beckett set you free."

"'Ve been cooped up in that damn infirmary for long enough. I'd have broken out if he'd tried to keep me in there any longer," he replied.

"You look well," I commented, noticing the scaly, purple skin was gone.

"Well, according to my DNA, I'm 100 percent John Sheppard again," he replied before looking at his arm. "Although I've got to say, I'm looking forward to getting rid of this thing one day."

"That should clear up eventually, the rest of it did," I shrugged.

"Yeah, that's what Beckett said," John nodded and then sighed as he continued to stare at his puncture scar. He reached up and rubbed the back of his neck with his other hand. "So listen… while I've been lying there and staring at the ceiling the past few weeks, I've been remembering things… some things I might have done that you could call out of character."

"Yeah," I agreed. "You could say that."

"I uh, Beckett and Weir commented you didn't leave my side the whole time I was out but I didn't see you again when I woke up. I can't help but feel like I've made things awkward between us and I wanted to apologise. While I do like you, I mean really like you, none of what happened over the past three weeks was how I wanted things to go. Don't get me wrong, I don't have any regrets over how this thing started, but things took a turn when the retrovirus started taking over."

"I noticed," I replied and he nodded awkwardly. I don't care if he was himself or not, he wasn't getting away that easily.

"I want you to know I'd never do something like that to you. I care and respect you so much, Captain, and it's scary enough having something like this happen with your CO but worse after what already happened with Torrell. And I want you to know I'm completely, and wholeheartedly sorry for any damage I may have caused and for hurting you when that's the last thing I ever want."

"I know you're sorry," I replied. "I uh, I understand most of it was the Iratus half of you. But I wanted you to say it anyway, say you're sorry. And I hope you don't mind me kicking the Iratus part of you in the nuts."

"Deserved it," he shrugged. "Deserved more actually. The way I see it is I got off lightly. Are we okay?" He asked gently.

"Yeah," I nodded. "I forgive you John, I do.."

"But?" he asked, sensing my hesitation.

"This was a lot before," I said. "I like you too but something like this with my CO, it's a big step and it's something I need to be sure about. And I'm not. I need some space. After what's happened..I just.. Look, if you want to leave it as a one off, I understand. Because I just can't right now."

"No," he shook his head. "No, I completely understand. Take the time you need and if you decide you don't want this, or me, I understand about that too. But this isn't just a one off for me. I like you, Evelyn, and I'm willing to wait."

"Atlantis was supposed to be my fresh start," I sighed, running my hand through my sweaty hair. "I should have known better, you're my CO. I can't fuck this up by having a rocky relationship with my boss…"

"No, no, Evelyn there is no rocky relationship," he said. "I'm not going to ruin your life over this. If you know now that you don't want me then we'll say no more about it. Things can go back to the way there were and I'm not going to stand in the way of you or your career."

"No I know," I told him. "I just. I don't have another option. This is the only way I can keep what I lost.."

"I understand," he told me.

I turned to leave, walking towards the door when I thought back to those flashbacks I'd had when he was eating me out. The messy way his hair sat now, I was sure I'd seen him before I met him now. Although I didn't quite understand why.

"You know," I said, turning back to him. "I'm sure we hadn't met before you interviewed me for this mission, but I can't shake the feeling I know you a little better than that."

"We did get to know each other pretty well a few weeks ago," he joked and I rolled my eyes.

"Goodbye John," I said and walked out of the gym to go shower in my quarters.

I sat at the bar, a thin sheet of liquid coated the wooden surface and made my arms sticky. I peeled one of them off the wood and gestured to the bartender to bring me another round.

I put the glass up to my lips, glancing back at the door as the amble liquid went down surprisingly smoothly for free, air force provided whiskey. My lieutenant was long gone, the rest of my team had had to escort him back to base after getting absolutely wrecked in the drinking contest we'd had.

"Can I get you another round?" a voice slurred beside me. I looked up to see the charming face of a slightly older male, whom I almost just told to fuck off, assuming he was a skeeze. I shook my head at the joke.

"Sure," I rolled my eyes.

"What brings you to the bar, drinking alone?" he asked and I smiled to myself.

"I'm the last one standing," I winked. "No one else seems to be able to keep up."

"Woman after my own heart," he replied. "You up for another friendly competition?"

"You sound like I could beat you easily, you never said what brings you to the bar, drinking alone," I countered, looking him up and down. While friendly and unthreatening, mystery guy looked like he was already pretty hammered.

"I'm not drinking alone," he said. And I scanned him over. His formal uniform had a few medals on it, and he wore the rank Major. "I'm here with you."

"Okay mystery Major, keep your secrets, I don't care," I told him. I placed my empty glass on the counter and the messy haired stranger waved over the bartender again, getting himself another beer and refilling me.

"I just got divorced," he relented.

"And are you celebrating or mourning?" I raised an eyebrow and he looked distastefully at me. I sighed and spun my glass around on the bench a couple times. "Divorce huh?" I glanced back at him. "Well, I can't really help you with that one. I've never been married. But, as someone who's a child of divorse, maybe this'll help. When you're married to someone who isn't right for you, you don't only hurt each other but the people around you. And although you know it's over, there's still a part of you that is always gonna care about them. That's rough and it's painful but I can promise you, you're both better off."

"You sure about that?" he asked.

"My parents were a lot better apart than together, I can tell you that without a moment's hesitation," I agreed. "You love her and that's okay, part of you is always going to. But it's going to hurt less."

"You're a bit young to be this wise," he said and I scoffed. "Sure I can't tempt you to a drinking contest?"

"I think I've had enough," I told him. "But if you wanna get out of here, Major, I might be able to help you forget for a little while."

"Forget huh?"

"A damn site better than this crap," I shook my glass at him.