Author's Note: Italics signify thoughts or emphasis. Part 5 of 5.

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Elizabeth stood in her office, trying to think of what could possibly be done. Trying being the operative word. Her brain refused to work. She had been standing in the same place for nearly an hour. She knew her chair was right behind her; it had been pressing against the backs of her knees the whole time. But somehow she couldn't force herself to sit down.

She couldn't sit at her desk in her office, reports piled in front of her, and pretend this was just another problem. She couldn't deal with this, because then she'd have to deal with being alone. With the fact that she had lost more than a second in command. As much as John had been on this expedition in the first place by sheer random genetics and then thrust into a position of command by the untimely death of another, he had given more than his all, more than anyone should be expected to give.

At every turn he had gone beyond the call of duty, calling on reserves no ordinary man possessed in order to keep Atlantis and its people… and her… safe. They sometimes disagreed and argued over the way to do certain things, but they respected each other's opinions. She knew with him that he listened to her, not merely nodding absently while planning his own moves like other military personnel she'd had experience with. He supported, protected and encouraged her. And he had become the best friend she'd ever had. More than that…

"Dr. Weir!" a voice crackled on her headset.

Snapped out of her thoughts, Elizabeth responded, "Yes, Sergeant Matthews?"

The sick feeling in the pit of her stomach intensified. Matthews had been left in charge of the men on guard duty.

"Ma'am, Colonel Sheppard has escaped his quarters. He broke out through one of the windows. As far as we can tell, he climbed along the outer wall to an uninhabited room a few doors down. Ellison was stationed down the hall and tried to stop the Colonel, but he… Ellison's dead, ma'am, and two others are seriously injured. Beckett's on his way."

"Stay with the injured men, Sergeant. Major Lorne will take things from here."

"Yes, ma'am. The Major has been updated as well."

"Thank you, Sergeant."

Elizabeth sat abruptly. She lowered her head, burying her face in her hands momentarily. This was her fault. She should've had him transferred to the holding cell after he killed Ford protecting her. Her refusal to give up hope that John would be okay had now resulted in the loss of an innocent life. Knowing she'd have the rest of her life for self-recriminations and guilt, Elizabeth put the steel back in her spine.

"Any indication of where he's headed?" she asked over her headset.

Major Lorne's voice responded after a crackle, "We believe the 'gate room, ma'am."

"Follow at a safe distance and tell me if he changes direction," she ordered before leaving her office for the control room. "Give me citywide." She waited until receiving a confirming nod from the man at the main console. "Attention Atlantis, this is Dr. Weir. Colonel Sheppard has escaped and is making his way to the 'gate room from the residential corridors. Please stay inside whatever rooms you are in with the doors locked and keep the halls clear. We don't want any unnecessary confrontations. I will give the all clear as soon as possible. Thank you."

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Ronon made his way to Elizabeth's office as soon as she made her citywide announcement. She was standing behind her desk with her arms loosely crossed over her stomach, her hands wrapped around herself. Her face was sad and thoughtful. Ronon cleared his throat to get her attention.

"What are you going to do?" he asked when she looked up at him.

"I don't know," she admittedly quietly.

Ronon shifted uncomfortably, aware of the closeness between Elizabeth and John through his observation of their interactions even if he was not sure of its full context. But he couldn't let what Elizabeth might be feeling stop him from saying what needed to be said. He was a very practical person when it came to survival; seven years running from the Wraith tended to do that to a person. And maybe she needed him to say it since no one else was going to.

"You only have three options," he ventured.

Elizabeth's eyebrows drew together, "You thought of a whole three? I haven't been able to come up with anything at all."

"You can keep him locked up in that holding cell for the rest of his life, send him to an uninhabited planet through the Stargate, or kill him." Elizabeth flinched, but Ronon pressed on. "If you choose either of the first two options and he ends up needing to feed like the Wraith or those bugs, you'll be condemning him to a slow, painful death through starvation."

Elizabeth was silent for long minutes, jumping slightly when one of her underlings stuck his head in for a moment to tell them that Colonel Sheppard had entered the 'gate room. She squeezed her eyes shut tightly, swiping away the single tear that escaped to trail down her right cheek before looking back up at Ronon.

"Would you…" she trailed off.

Ronon nodded tersely and turned to head for the stairs that led down to the floor of the 'gate room.

"Ronon," Elizabeth called. He turned his head. "Make it as quick as possible."

He nodded his head once in acknowledgment.

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Elizabeth forced herself to follow Ronon out and move to her oversee-the-returnees spot to watch. She hugged her arms to her stomach tightly, reminding herself that he was no longer John. And even if a tiny piece of him still was, the part that had protected her from all threats, this was a more humane ending than any of their other choices. It was what John would have wanted.

After a first… last look at John, her eyes trailed Ronon as he slowly moved toward the mutated Colonel. It was over quickly, just as she had asked; Ronon using what she assumed was his weapon's highest setting in three quick, successive bursts. Elizabeth felt every shot as if they were hitting her, a small part of her dying inside as the being that had once been John Sheppard fell for the last time.

A fist had closed around her heart when right before he had turned to watch Ronon approach, John had looked up at her like he always did before and after off-world missions. She had to keep reminding herself that very little had been left of the real him, and within days, or even hours, there would have been nothing of John Sheppard but a new, very dangerous species.

Elizabeth sent a subdued message to Carson to come get the body before telling one of the civilians in the room that she was leaving him in charge until her next shift. Elizabeth took the comm device out of her ear and left it on the closest desk.

She had someone to say goodbye to.

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The broken window in John's room had already been covered up with what look like the top panel of a packing crate when Elizabeth got there. The violated glass was the only thing that showed any hint of what the room's inhabitant had become. That and her jacket at the base of one wall, as if it had been thrown against it. Had he felt betrayed waking up to find her gone? Was he even capable of feeling betrayal at that point?

Everything else was much like it had been every other time she had been in his room. The bed was made with military precision, and though some things weren't put away, the room felt lived in rather than messy. Elizabeth wandered aimlessly through John's possessions, trailing a hand over different things. He'd managed to smuggle in more of his things when they'd come back from Earth on the Daedalus, as each of them had.

A small smile of remembrance lifted the corners of her mouth as she passed the long board leaning against one wall. When things had calmed down after the storm during which Kolya and his Genii invasion team had tried to take Atlantis, John had told her that he had never seen waves that big. That any surfer would have given his or her right arm to be able to explore all the beaches of the mainland directly after the storm had passed. John, of course, had been too busy with his duties to take advantage of the change in surf, but he'd promised in passing to teach her how if they ever both had downtime when they could get way from the city.

Her heart squeezed painfully as Elizabeth wondered if there ever would have been such a time if he had survived the infection. She moved away from the board, heading with watery eyes for the bed. She sat quietly for several minutes until the tears that had threatened were under control.

'War and Peace' sat on the nightstand, the bookmark indicating John's progress not even close to a quarter of the way through. She reached for the book absently, letting out a small gasp when a paper wedged underneath it fell to the floor.

Elizabeth leaned forward to retrieve the folded sheet, the tears welling once more in her eyes when she saw her name written in John's masculine scrawl. There were two pages folded together, and Elizabeth opened them, careful not to let her falling tears mar the paper.

Elizabeth,

I'm writing this now, when all that has changed is some of how I look and a bit of an increase in strength, so that it is done for later when I no longer have the mental faculties to be able to do it. I know you still hope that Carson will find his miracle cure, but I've accepted that it's already too late. No matter what happens, I know you'll do the right thing. I have no right to ask any of this of you, but I hope that what we might have…would have shared if things had continued to progress is as clear to you as it is to me. If our positions had been reversed, which I never would have wanted, you know I would have taken care of everything for you.

Please apologize to anyone I might have hurt. Let the people who are important to me know that I wish them the best. When Carson's done with my body, remind him it isn't his fault, and then cremate me. I'd like my ashes dropped off our balcony where the older you was let go. Send one of my tags back to Earth, to the Air Force, as is called for by procedure, but I'd like you to keep the second one if you feel comfortable doing so. I'd also like you to have anything else of mine you'd like to keep. Hey, maybe you'd like my room; it is bigger than yours. I suppose under the circumstances I shouldn't tell you that the thought of you sleeping in my bed makes me smile, but it does.

Elizabeth couldn't help the small grin that broke through her tears. It was such a John thing to say. She could picture the playful smirk that would have been curving his lips as he wrote it.

My biggest fear now is that everyone will remember what I became instead of who I was. I take comfort in the knowledge that I know that isn't true of you. I think a part of me, the best part, will live on in your heart. Coming to Atlantis may have been a fluke of genetics, but it became home… my city. General O'Neill once told me that he thought anyone who didn't want to step through the Stargate to different worlds was insane. I feel the same way about anyone who would say no to the adventure of life in the Pegasus Galaxy. When I think about all the things I wouldn't have seen and done and learned if I hadn't taken that risk… not the least of which was getting the chance to know and work with you… I know I made the right choice, despite how it ended for me.

I hope they send you someone who unlike Caldwell actually has a beating heart, who cares more about the people in his command than the position he has, but even if you get stuck with him, I know you'll keep him in line. Look at what you were able to accomplish with a maverick like me beside you. You're a great leader, Elizabeth, and I want you to always remember that. Never let anyone forget the importance of this expedition. But most of all, don't forget to take the time to appreciate the wonder of all you see and do and try to think of me in those moments.

Yours forever,

John

The sheet of paper that followed the letter was a dry list of his last wishes, signed 'Lt. Colonel John Sheppard.' The letter was just for her, the list a way to let her follow his requests without anyone else intruding into this last private thing between them. There would be talk when she kept one of his tags and moved into his room, keeping most of his things, but he was gone and no matter what anyone said or how they felt about the situation, John was no longer here.

Neither one of them would be replaced because of their feelings. And Elizabeth would hold onto these last pieces of him with all her strength. She would need the connection to him to make it through the coming years and be able to make the right decisions for their city. The word love had never been mentioned by either of them, but Elizabeth knew it was what he was referring to in his letter. She knew that even though she hadn't said it, he had known how she felt. He hadn't wanted to sully the emotion by simply writing it, and in a way she was grateful for that.

With a heartfelt sigh, Elizabeth folded the letter and put it back under 'War and Peace' for later. She stood, the list clutched in her hands, ready for her to begin implementing his wishes. Elizabeth cast a quick glance around. She would be back, and soon, but this was the last time it would be anything but her room.

"Goodbye, John," she whispered.

The End.