A/N – This was originally completed with chapter 3 but I had several people tell me that it felt incomplete, that the ending was too abrupt. Considering that this started out as a one shot that somehow morphed into a multi chapter story, I figured, why not? So, here's a new ending, hope you like it! Feel free to let me know what you think…wink…wink.

~,~,~,~

Epilogue

The sound of his raspy voice caused Ronon to drop his feet from the bed, practically exploding from the chair he'd been dozing in. On the other side, McKay also jumped to his feet, his precious laptop hitting the floor unheeded as he shouted. "You're awake! You're finally awake! I need to go get Carson!" With this pronouncement, he scurried from the room.

Sheppard's eyebrows shot up at the commotion and he looked at Ronon who only stared back at him, his face a blank mask. John frowned at him and watched as his friend stiffened and then turned way, starting to leave. "Ronon?" When there was no response, he tried to raise his voice but found it much weaker than he would've liked. "Ronon!" The man stopped but didn't turn around. "What's going on?"

Facing away from him, the Satedan responded. "I know you don't want me here. I'm just glad you're finally awake."

"Why wouldn't I want you here?" He had a feeling he knew why.

Ronon turned, a look of disbelief on his face. "Why would you? I turned on my Commanding Officer. Not only that, I turned on my friend. I sided with Kanaan against you."

John remembered Atlantis's words. "You had no choice, buddy. Kanaan had control over you." He looked at Teyla who had yet to say anything, tears still running down her face, Torren on her hip gurgling at him, the only one who seemed calm at the moment. "Over all of you! None of this was your fault. Any of you!"

"I should have been stronger! I've been forced to be a Wraith worshipper, under their control! I know what it feels like! I should've known something was going on, I should've known that you'd never do what he accused you of, yet it never entered my mind to believe you instead of him." The last words were said with self-disgust.

"And that's on Kanaan, not you! I know you'd never turn on me willingly! You've saved my ass too many times over the years. I know you, you're one of the most honorable men I've ever met." Ronon hmphed and folded his arms across his chest, unwilling to let the man he thought of as a brother, a man he'd let down so badly, let him off the hook that easily. "Look, I've been there! When that damn retrovirus started turning me into a bug, when Thalen took me over and tried to use me to kill Elizabeth, when the crystalline entity came back to Atlantis with me after I stupidly touched it, don't you think I had regrets about the things I did while under their control? Regrets I still have? Don't you think I worried that no one would ever be able to trust me again? But you did, you all did. How could I do any less?" His speech tired him more than he wanted to admit.

Ronon blinked as he processed his friend's words. He dropped his arms to his side and tilted his head to the left. John waited while he thought. When a slight smile appeared, he knew it would eventually be okay, even if it took some time, they were on the right track now. He might have some moments of bitterness in the future, but Atlantis had been right, his friends, his family, were not to blame and they were worth it. He turned his attention to Teyla, who had yet to say a word. "Teyla?" His voice cracked and she quickly moved to the table by his side, picking up a cup of water with a straw in it. She wordlessly held it to his lips and it dawned on him just how thirsty he was. He sucked greedily at the water, frustrated when she took it away too soon. He tried to lift his hands to pull it back and barely managed to get them more than an inch of so off the bed. He frowned and she leaned forward to brush a hand gently down the side of his face.

"You cannot have too much too soon, John. You need to wait for Carson."

"Why?" He hated how whiny he sounded.

"Ye've been ill for quite a while, laddie! I need to check ye out before I allow any more." Carson had returned with Rodney without John noticing it, his attention focused on his team mates.

"How long is quite a while, Carson?"

"A little over three weeks."

"Three weeks!" To say John was stunned, would be an understatement. "Why so long? What was wrong with me?"

Beckett cleared his throat. "Ye were beaten severely and almost died several times. I had to fight to keep ye here with us. Yer body needed time to heal." John watched him, knowing he was holding something back.

"And?"

"And what?"

"What aren't you telling me doc?"

Teyla spoke. "Carson believes you did not want to come back John. That you did not want to come home to us." Her voice broke a little.

He was silent for a moment, knowing that the doctor was right. He hadn't wanted to come back until Atlantis had made him see it was wrong. He tried to reach out to her and she instantly took his hand in hers. "That might be true, but someone very smart made me see how wrong that was. I belong here, with you." He turned and looked at them all. "With all of you."

The relief in the room was palpable as they all started to talk at once. Carson raised his voice a little. "All of ye, out now. I need to check John over. Ye can come back later. I think it would be a good idea if ye finally got something substantial to eat and some rest. Now shoo!" Each reached out to touch him as they said their goodbyes, almost as if they needed to be reassured he was really there. When it was just the two of them, he went into full doctor mode, taking John's vitals, checking his blood pressure and, when he was satisfied that all was well, raised the back of the bed so his patient could sit up a little. "Ye'll need to take it easy for a while John, yer body underwent a severe trauma and ye haven't moved around much in weeks. Ye'll be weak and, knowing ye, very frustrated, but ye must take yer time!" He helped John drink some more water until he'd finally had his fill.

John thought of something. "Carson, why was Rodney unaffected?"

"We think it was the ATA gene. Neither Rodney, Lorne, Sgt. Stackhouse nor meself, among others, were affected, other than a bad headache."

"How did you reverse it?"

"How do ye know it was me?"

"First, you're one of the best doctors I've ever known, if anyone could figure out how to deal with it, it would have been you."

Carson waited. When the room was quiet for a few moments, nothing more forthcoming from the colonel, he prompted. "First?"

John swallowed. He still wasn't sure if he wanted to share what had happened in the last moments of his unconsciousness, worried that they'd think he was brain damaged.

"Colonel?" Carson tilted his head at him.

"Fine, someone told me." If John had been able to move, he would have now been the one folding his arms over his chest.

"Someone? Ah, Ronon, Teyla or Rodney?"

"Um, no." He knew Carson, knew he wouldn't let it go and would ask each of them if they'd been the one to inform him of what had happened.

"Then who?"

"I don't know if you'll believe me if I tell you."

"Why don't ye try me? I've seen things in this galaxy that I'd never thought would be possible." He paused. "John, I'm yer friend as well as yer doctor. Ye can tell me anything."

"Fine, Atlantis told me." He waited for the doctor's response. When it came, he knew he shouldn't have been surprised.

"Was she also the one who told ye it was wrong to stay hidden away from us?"

John blinked a couple times. "Yeah, it was and I never said Atlantis was a she."

"Ye didn't have too. Ye're not the only one with the ATA gene. I've always suspected that the city had its own consciousness and I've always thought of her as female. It was just a feeling that she was alive and happy to have us here with her."

"Really? Why didn't you ever say anything?"

"Well, it's a wee bit of a stretch, don't ye think? Wouldn't do to have people thinking the doctor was barmy, now would it?"

John looked him in the eye and then smiled, Carson joining him. It felt good to be back.

~,~,~,~

The next day, Carson stood at his side again. Even though he'd been unconscious for more than three weeks, John felt tired all the time and had fallen asleep shortly after his conversation with his team mates and the subsequent one with the doctor. He'd slept all night, this time a natural and healing sleep, and had only just awoken again. "Colonel, do ye feel up to some more visitors?"

John yawned and blinked as he nodded. Carson raised the back of the bed again and left. He heard voices outside the privacy curtain and then it moved aside to let Richard Woolsey and Evan Lorne in. His gut clenched as he remembered being relieved of duty. While it seemed that everything was back to normal, he still wasn't sure how to deal with the expedition leader. "Mr. Woolsey." He said guardedly.

Woolsey winced and sighed. Taking off his glasses, he polished them nervously on his uniform. Putting them back on his face, he met Sheppard's eyes. "Richard please, Colonel. I'm here to tell you how sorry I am about what happened. I can't imagine anyone else in command of Atlantis's military and I hope you can find it in your heart to forgive me. You were fully reinstated as soon as the retrovirus released us from Kanaan's control. I've brought the SGC up to speed on what happened and they backed me one hundred percent."

John had to chuckle. "Bet Caldwell was pretty frustrated by that! He's come so close, so many times, to finally getting to be the CO of this base."

"Perhaps, but I will tell you that Colonel Caldwell was the first to say that reinstating you was the right thing to do."

"He did, did he?"

"Yes. Look, Colonel…"

"Richard, I thought we were past that. You used to call me John." With that, he let Woolsey know that he'd accepted the man's earlier apology.

"John." For the first time in weeks, Richard felt a weight lift off his shoulders. "I really am sorry. I've always prided myself on being a logical man, but what happened, what I did, was NOT logical."

"And not your fault." John turned to Lorne, indicating that that line of conversation was over and behind them. "How'd you like being in charge, Major?"

"Relieved you're awake and can take it back sir! I believe I like being 2IC better. Mr. Woolsey actually threatened me with having to do evaluations!"

John chuckled, understanding exactly what Lorne had been feeling. "I guess that means they're not done and I'm still stuck with them?"

Lorne grinned from ear to ear. "Yes sir!"

The two men smiled at each other and then John's curiosity kicked in. "Richard, what happened to Kanaan?"

The man sighed again, not sure how the colonel would take the news. "We didn't quite know what to do with him, to tell the truth. He was not under my command or yours so, technically, wasn't subject to our discipline even though he lived here on Atlantis. There's nothing in the regulations about how to deal with someone who used mind control to influence other people and force them to attack another. I brought in Halling, who is very happy to hear that you're awake, by the way, and told me to tell you Jinto sends his well wishes. They would both like to visit when you're feeling up to it."

Realizing he'd gotten off track, he continued. "Anyway, Halling agreed to take Kanaan back to New Athos and deal with him as an Athosian. He could have been banished, but the council felt that there were mitigating circumstances after having been used against his will by Michael. The man who did this was not the man they used to know. In addition, he is Torren's father and they didn't want to have the child grow up with that stigma. From what I've been told, Kanaan is being a model citizen, doing his work and keeping to himself. He hasn't expressed any remorse over his actions, but then he hasn't spoken much since Ronon knocked him out with his blaster."

"Ronon shot him?"

"Yes, apparently he went after Dr. Beckett when he realized he'd lost all his powers, including the one he was born with, the one he shared with Teyla."

John thought about it. "That's gotta be tough, to lose something that has been a part of you your whole life."

"I would imagine, but he brought it on himself."

"Did he? Or did we bring it on? Without us, there would've been no Michael. The Athosians would still be whole, never would've suffered at his hands. Teyla would never have had to kill Michael to protect Torren from him."

Woolsey nodded, knowing that many of the expedition members still felt guilt over what had happened. The old expression, the road to hell is paved with good intentions, passed through his mind. Straightening his shoulders, he said. "Well, now that we've cleared the air, I have a lot of work to do. I'll leave you two to talk." He reached out to shake John's hand and had to grab it when John could only get it off the bed so far. He nodded at Lorne and took his leave.

"Lorne?"

"Yes sir?"

"Sit, will you? You're making me nervous."

"Me? Making you nervous? That'll be the day." Evan huffed out with a laugh as he sat in the chair by his CO's bed.

"So, tell me what's been going on? What've I missed?"

"Well, when Kanaan was still in control, I spent most of my time breaking up fights between ATA gene carriers and non-carriers, military or civilian, didn't matter. Once the situation was under control, I had to squash the 'I told you so's." He paused. "There are many who would like to tell you they were sorry, even if they never did anything directly to you." He knew what would be coming next.

"And the ones who did do something directly to me?"

Lorne sighed. "Jennings, Manning, Johnson and Delaney. They confessed immediately after the doc's retrovirus worked, even placed themselves in custody."

"You know it wasn't their fault?"

"I know that, you know that, but try convincing them of that! They all admire and like you, they can't figure out how they could've done what they did."

"Did you tell them about Kanaan?"

"Of course, doesn't seem to have made a difference."

John sighed. "Where are they now?"

"Holding cells."

"What? Why would you leave them there?"

"I didn't! The door isn't even locked! They just won't leave, except to sit with you and cover their duty roster. Once they were off duty, each one headed back to the holding cells. Since you finally woke up, not one of them has left there." Lorne had tried to get through to them, but not one would budge.

"They all disobeyed your direct orders to return to duty?" This bothered him more than the beating. Lorne's eyes dropped and he fidgeted in his chair. "Lorne?"

Lorne stared at the privacy screen across from him, not meeting his CO's eyes. "Well..."

"Evan, what's up?"

"I may not have given them a direct order to return to duty."

"Why?"

He risked a look at Sheppard and saw only curiosity, no condemnation or disappointment. "I...I guess I empathized with them. When I was taken over by the crystal entity and was sleep walking, I really thought you were a replicator and wanted to destroy you."

"But you didn't."

"No, I was lucky. If things had gone differently..."

"They didn't and even if they had, you weren't responsible."

"I know that but I can imagine how I would have felt and I could see myself feeling exactly like these men do. I couldn't bring myself to order them to do something I would have refused to do."

John sighed. "Okay, bring them here to me, in shackles."

"Sir?"

"Just do it Lorne!"

Evan reached up and activated his comms. "Sgt. Stackhouse?"

"Yes sir?"

"Would you please bring the prisoners up to the infirmary, in chains please?"

"With pleasure sir!" Lorne grimaced at the pleased tone of the younger man's voice.

"Evan?" He was frustrated that he didn't have his comms and had to rely on someone else to tell him what was going on.

"Sorry sir, Sgt. Stackhouse seems to have taken this very personally. He wants all four to be brought up on charges and send back to Earth immediately, even knowing they weren't in control of themselves."

"He's a good kid."

"I know that John, I just wish he'd be a little less combative about this."

"I'll talk to him too." John had a feeling he would be dealing with the fallout from this for a long time to come. While they waited, his 2IC brought him up to date on everything that had gone in Atlantis while he was out of commission, including the latest gossip.

"She did what?" John asked, laughing at a bit of gossip about a love triangle that was forming between three scientists, when Stackhouse arrived with his charges. None of the four would look him in the face, although all four stood ramrod straight. "Okay, everyone else out." Stackhouse looked mutinous but Lorne dragged him out of the infirmary. John stayed quiet, waiting them out.

Finally Jennings couldn't stand it any longer and raised his head. "Sir, I…I don't know what to say or how to apologize! I want you know that we'll accept any punishment you deem necessary."

"Captain, do you harbor any ill feelings towards me right now? Do you feel I'm unfit to command?"

"No sir! Just the opposite in fact! You're the best CO I've ever had! I've enjoyed working for you here on Atlantis, more that anyone I've ever worked under. I'll miss it."

"Then you accept my authority?"

"Yes sir!"

John looked at the others. "Do you all feel that way?"

A chorus of 'yes sir's met his question. "Very well. I've decided what your punishment should be." All four waited, looking downcast. "You will be forced to stay on Atlantis and continue to work under me. You will understand that nothing that happened was within your control. You will also all meet with Dr. Straub, the base psychologist, who will, hopefully, help you to see that this was not your fault. I've already forgiven my team for what happened. Can you accept that I don't hold you accountable?"

"Sir, we did what we did."

"Yes, you did. And I did what I did. I attacked Teyla in the gym when I was mutating into a bug, I tried to kill Dr. Weir while under the control of Thalen, do you think I should be sent away? Made to pay for what I did when I wasn't in control of myself? If you believe you need to be punished, then I'll submit myself for the same punishment and resign my command here."

"No, sir! You can't do that!" Manning burst out. He'd been here from the beginning, coming to Atlantis under the command of Colonel Sumner, a man he'd respected but had found to be rigid. He doubted they'd all still be alive if Sumner had remained in command. He'd been on Athos when they'd first met the Athosians, trying to find a place to bring their people to as the city was failing but, instead, had brought the Wraith down on them. He'd seen Sheppard refuse to give up on the people who'd been culled as he fought with Dr. Weir to be allowed to mount a rescue, and rescue most of them he did. He'd heard about what had happened during the storm that had forced all of them off the city, leaving it open to the Genii and Kolya to almost seize control. The man in the bed could think on his feet and adjust to any situation at hand, better than anyone he'd ever seen. That was what was needed on Atlantis, not someone like Caldwell, who he knew would be on the short list to take over. In fact, he was pretty sure Caldwell was the list.

"Very well, that's your choice, do you accept your punishment or do I resign?" He raised an eyebrow.

"Sir, why would you do that?" Asked Johnson, the one with the least tenure on Atlantis. He'd heard the tales of the things the Colonel and his team had done, but he'd taken a lot of it with a grain of salt. He had, however, seen some things with his own eyes that had cemented his admiration of his CO.

"I would do that because I've been where you are. I was not held accountable for things that were out of my control. How much of a hypocrite would I be to hold you to a higher standard?"

Jennings pulled in a deep breath, finally daring to hope. "Sir, I would like to state I'll take the punishment of working under you for as long as you'll have me." The others nodded. John hid the relief he felt. He'd have had to follow through if his men hadn't accepted his offer and the last thing he wanted was to ever leave here.

"Very well." He raised his voice. "Stackhouse?"

The man popped into the infirmary, confirming John's instinct that he hadn't gone far, regardless of his orders. "Sergeant, please release these men from their bonds."

"Sir?"

"You heard me, they are to be released and allowed to go back to their duties."

The man stiffened but did as he was ordered. He undid the locks on each man silently and watched as each saluted their CO and left the area. He started to follow when John called him back. "Sergeant?"

"Yes sir?"

"Look, Phil, I know you don't agree with me and I'm honored that you feel so strongly about punishing those who hurt me, but you have to know they wouldn't have done what they did under normal circumstances."

"Permission to speak freely sir?"

"Always."

Stackhouse started to pace. "With all due respect, Colonel, you didn't see what they did to you! I was on first watch when we were afraid to leave you unguarded. You looked like there wasn't an inch of your body that wasn't damaged! How can I trust someone who did that?"

John sighed. "Do you trust me?"

"Yes sir! With my life sir!"

"You know the things I've done when I wasn't myself?"

"Well, yes sir, but…"

"No buts son, they are not accountable for what happened any more than I was. I'm hoping you can trust me enough to come to terms with that. I need you here at my side."

Stackhouse puffed up a little at the compliment, as John had hoped. "I'll do my best sir!"

"That's good to hear. Any time you find yourself doubting that, come and find me. My door is always open."

"Thank you sir!"

"You're welcome. Now, dismissed. I'm thinking there's a nap in my very near future." He winked at the younger man and was relieved to see an answering smirk. Stackhouse nodded and left the infirmary. John leaned back and sighed, exhausted.

"Ye did good there, laddie." John turned his head to find the doctor coming around the privacy curtain, stethoscope around his neck.

"Carson? Eavesdropping?"

"I was on my way to check up on ye and stopped when I heard voices. Major Lorne had filled me in on what was going on with those men and I was curious to see how ye dealt with it." He was unrepentant about overhearing the conversation between the CO and his men.

"Well, thanks for the vote of confidence. I have to admit, I was a little worried they wouldn't take me up on my offer and I'd have to follow through and resign."

"Ach, I doubt there was ever a chance of that. Those lads just needed to hear it from your lips, no one else could make them accept what they'd done."

"I hope they can get past this."

"Well, they've taken the first step. Now, let's see how ye're doing." John lay back and submitted to the doctor's exam, falling asleep before it was over.

~,~,~,~

He was still sleeping when the light came again. This time he was prepared. "Atlantis?"

"Yes, I am here John."

"It's good to see you again."

"I am glad to see you as well. Are you feeling better?"

"I am. Thank you!"

"For what?" He watched the knowing smile he remembered, grace his mother's face.

"For giving me the kick in the pants I needed. I should've known that my team would never willingly turn against me without good reason. I was hiding for no good reason."

"I am pleased that you feel that way."

"I'm glad you're here. Does that mean we'll be able to communicate from now on?"

"Yes, you have taken the steps forward to allow us to speak at will. If you continue like this, we will be able to speak even when you are awake."

"I'd really like that."

"As would I. Your friends are greatly relieved. They missed you."

"I missed them too." He paused. "You said there have been others before me?"

"Yes, John, many others over the years, although there was a long, lonely time while I slumbered beneath the waters. Your appearance was most welcome."

He smiled. "I felt like I was coming home as soon as I stepped through the gate. Was that you?"

"Yes, your presence was so strong when you first stepped foot on me. I had never felt the connection so strongly, so quickly, even with my makers, those you term the ancients."

He grinned at her and was surprised at the answering grin. Atlantis seemed as human as him. "I'm glad to see you looking so pleased." He smirked.

"You have done well. I watched while you dealt with the men who grievously harmed you. It was masterfully done. I am not sure if I would have been as generous."

Even in his dreams, Sheppard blushed at the praise. "I was lucky and I do believe they are innocent of any wrongdoing. Still, it could easily have gone the other way."

"No, John, it could not have. You have the hearts of most here in the city. Those that do not agree, have their own issues. While most thought your Dr. Weir was the heart, many believe that you are the soul of your people. With her passing, you have taken on both roles."

"Um, well, thanks."

Atlantis shook her head, her smile widening. Before him, the ones she connected with had all been of the race of her makers. Sure of themselves and believing that they were always in the right. Never admitting to their mistakes. John Sheppard had shown her a different side of the species known as human. She found she liked this form better.

"Sleep now, John, we will speak again soon." The light faded as he drifted back into a deep sleep.

When he awoke again, the infirmary was quiet and in near darkness. He sensed her presence before she said anything, he always knew when she was near. "John?"

"Hi Teyla, it's good to see you! Where's Torren?" He saw she was alone, instantly missing the presence of the toddler.

"Ronon and Rodney are watching him. I asked to be able to come here to talk to you alone."

John sighed. "Are you going to apologize now? Seems like that's all anyone wants to do these days."

Her chin quivered and he worried that he'd hurt her feelings. "John, I know in my head that I am not to blame for what happened, but in my heart I find it hard to forgive myself."

He reached out a hand to her, already stronger than he had been when he'd first come out of it. She took it and held on tight. "Teyla, you trusted Kanaan, there's no way you could've known what he was capable of."

"I was the one who brought him here! I was the one who requested he be able to live on Atlantis with us. If I had left it alone, if I had just let him stay with our people on New Athos, he would not have been able to do what he did! You almost…you almost died because of him. I do not think I could ever have forgiven myself if things had turned out differently."

"He's the father of your son, Teyla. He's someone you've known all your life, someone you trusted. How could you have known this would happen?" He squeezed her hand and smiled at her. Suddenly he heard Atlantis in his head, remembering the things she had said to him. He knew Teyla was the one who was waiting for him with love. It was time for him to stop hiding his feelings. "Teyla? I…" He paused, still not comfortable with expressing his feelings, but knowing Atlantis was right, it didn't serve him well. He took a deep breath. "I need to tell you something."

"John, I need to tell you something as well and I would like to say it now, before I lose my courage."

"You're one of the bravest people I've ever met, I find it hard to believe you're afraid to tell me anything."

"I am afraid of this. Afraid it will change everything but I cannot keep it to myself any longer."

"Teyla?" He knew what she was going to say and was determined to say it first. His heart full, brimming with confidence based on his conversation with his city, he put himself out there.

"Yes John?"

"I love you too."

~,~,~,~

A/N2 – I have no idea what Sgt. Stackhouse's first name is and couldn't find it on the internet anywhere, so I went with Phil. Honus47 will know who that is! If someone knows what it really is, let me know and I'll update it.