Chapter 23: Change of Command

Elizabeth had no idea, but she was not going to be able to keep her promise. After getting a communique from Stargate Command, she learned that she was being replaced in favour of a military commander who would be able to ensure that the military mission and well being of Atlantis was being executed to the max. She was given twelve hours to pack and in that time she avoided everyone. Her quarters were first, and her office last. She knew that the people in the command centre were talking about her but she had no idea what was being said.

"Sheppard," Rodney began as he chased John up the steps to the main area of the gate room. "What do you think you're doing."

"I almost lost her once," John stated angrily, not caring who was listening. "I'm not going to lose her again."

"You're not losing Elizabeth," Rodney tried to explain. "She's just being recalled."

"She won't be here."

"You can't control that."

"Oh yeah?" asked John as he stormed towards her office. "Elizabeth?"

"Yes?" she asked as she looked up, noticing with some interest that John was standing in her doorway while Rodney was snapping at the people in the control room to get back to work. "Can I help you?" she continued, trying to be as professional as possible.

"Yeah," he continued as he stepped into her office and sat down in his usual spot. "You can help me by not leaving."

Elizabeth sighed. "I don't have a choice."

"You always have a choice."

"I can't defy an order."

"They can't make you go through the gate," John pointed out.

"They'd send marines to drag me through,"

"They'd have to get through me first." John muttered.

"Oh John," she whispered. "It's not... you can't—"

"Atlantis can't lose you."

Elizabeth shook her head. "Colonel Carter will be an excellent commander," she argued. "She knows how to handle military situations a lot better than I do."

"And what about me?" asked John. "I could command."

"You after my chair John?"

"All I'm saying is..."

Elizabeth laughed, though it was strained. "I know what you mean. But the decision has already been made. Colonel Carter will need you to give her the Pegasus intel. She's walking into a mine field here John what with the Wraith, the Asurand and—"

"I can't lose you," John blurted out, surprising them both. "You... you promised."

Elizabeth sighed and leaned back in her chair. "I know. But there's absolutely nothing that I can do. I'm employed by the IOA. I've been dodging this bullet for a while and to be honest... I can't fight anymore."

"Don't you want to stay?"

"You know I do," Elizabeth assured. "Don't you?"

John nodded. "I do it's just, I'm not used to seeing you give up."

"It's not like I'm giving up,"

"I understand that you have a lot to do and—"

"—John," she interjected, knowing that she had to say something to stop his babbling. "The only thing that I'm going back to is my mother and my teaching job," Elizabeth explained watching as John leaned back in his chair. "You have to know that there's no where in two galaxies that I'd rather be than here with you..." she paused and watched the flicker of surprise in John's eyes. "And the whole team," she amended feeling rather self conscious. "Atlantis is my home."

"Then do what you want."

"What I want isn't up for discussion," Elizabeth argued. "What I want doesn't matter."

"It matters to m— to all of us here," John assured, changing his sentence halfway through.

"I know, and I thank you... all of you for that," she stated, pausing a moment to look out int the control room. "But it's not like I'm never going to see you guys again. Technically I'm only a step away. You could always take some leave on Earth, god knows that you've got enough of it saved up."

John laughed, deciding to sideswipe the fact that she was all but formally asking him out on a date. "What are the chances that I'd actually be able to use it?"

Elizabeth laughed too. "True. It seems as though there's a crisis here every couple days."

John nodded. "And there is the flight back."

"The midway station is going to be completed soon," Elizabeth pointed out. "It would just be a step back to Atlantis."

"True," John stated with a sigh, knowing that there was nothing that he could do or say to change her mind.

There was one thing that John knew that he could say that would change things between them, but he wasn't ready. He had been holding off to say it for so long, he figured that a little longer wouldn't hurt. She was right after all. They would only be a step away from each other technically, and he wouldn't want to ruin anything by saying something in the heat of the moment that would have Elizabeth leaving Atlantis with the feeling like she owed him, or rather them something.

"I guess that you've got to finish packing?" he continued, dropping his gaze to the boxes that littered the floor around her desk.

Elizabeth nodded. "Yeah."

"Then uh, I'll see you at the gate?"

Elizabeth nodded again. "Yeah. You'll see me at the gate."

John stood up and made his way to the door before pausing. "Do you, do you want some help?"

"Oh yes," Elizabeth assured with a smile. "That would be great."

Their final moment on Atlantis just flew by. The orders had been given and Elizabeth's stuff had already been shipped through the gate. She had just given her last all-call goodbye and it was all that Elizabeth could do to keep her tears at bay. It was a task that proved to be even more difficult when John and his team minus Teyla of course, came up to her.

"I uh, just wanted to thank you," Ronan began as he stepped forward. "Thank you for letting me stay."

Elizabeth shook her head. "No need to thank me."

"Still," he continued. "It's been really nice having a home and, I owe a little of that to you."

"You're welcome."

Ronan and Elizabeth stood there awkwardly before Elizabeth made the first move and hugged the large Stateatan. "Goodbye Ronan."

"Goodbye Doctor Weir."

Ronan and Elizabeth pulled away and Elizabeth turned to Rodney. "Dear Rodney," she began with a smile. "It sure has been a journey."

"I want you to know that I've lodged a formal complaint with the IOA," Rodney stated in a nervous tone. "And I've even sent them bits of my book..." he paused and noticed the look on Elizabeth's face. "Oh don't worry, nothing of a personal nature but I uh...I just thought that they should know from me what a great leader you've been and well, we're all going to, that is to say..."

"I'm going to miss you to Rodney," Elizabeth stated as she gave her long time friend a hug.

"Goodbye Elizabeth," he stated as he pulled away. He and Ronan then left the gate area to watch from the control room giving Elizabeth and John the space to say their goodbyes alone.

Elizabeth sighed. "Guess this is it,"

"Guess it is,"

Elizabeth blinked back the tears that were prickling in her eyes. "Goodbye then?"

John nodded. "For now. When I get Colonel Carter to approve some leave I'll uh, come visit you."

Elizabeth smiled. "I'd like that."

They stood in silence before they both reached forward at the same time to hug each other.

"Oh I'm going to miss you,"

"I'm going to miss you too Elizabeth." John agreed. "It's not going to be the same with out you."

"You'll manage."

"That's not the point,"

"Then what is?" asked Elizabeth.

"You're the only one who's believed in me enough to give me a second chance," John stated as he pulled back to look at Elizabeth. "In the process you've become a dear friend and I uh—" he paused, losing the nerve to say what he so wanted to say. "—I don't know what I'm going to do without you."

Elizabeth choked back a little sob and tried to put on a smile for John's sake. "The feelings mutual..." she whispered as she stared longingly into John's face. "Now I've got to get out of here before I lose my nerve," she continued as she took a step back. Elizabeth put on her brave face and gave a smile and a wave to all the people who had gathered to see her off. "Goodbye everyone," she stated loudly enough for them all to here. "Stay safe. I'll miss you all."

And with that said, Elizabeth turned and walked towards the gate. She paused momentarily to glance back at John and he was surprised to see that she stepped through with a single tear rolling down her cheek.

...

John didn't return to the gateroom until he heard that Colonel Samantha Carter was moving into her new office and wanted to meet her second in command. He came barging in, determined to give his new boss a piece of his mind. "Welcome to Atlantis Colonel," he stated as he walked through the door. "Now I just want to say—"

"Wait," Sam interrupted. "Let me have my say first. I know that you don't want me here and Colonel Sheppard you should know that I don't want to be here either. I had a life back on Earth. I had friends and a family and after we defeated the Ori I got promoted. The promotion also gave me this post and while I could have turned it down, I didn't."

"May I ask why?"

"Because I knew what was going on here," Sam stated. "You may find it hard to believe but since you regained contact with us I've been corresponding with Rodney and he's kept me informed. I've known about everything and I knew that if I didn't step up the IOA would have chosen instead and it would have been a disaster."

"Disaster?"

"I'm on your side Colonel," Sam assured. "The brain from Washington that the IOA was considering for this position would not have been so understanding about the way things are done around here."

"Colonel Carter,"

"Sheppard I am not your enemy," Sam interrupted. "I can't have you being mine. I need your support. You've been the leader of the military here for almost four years and you've got the support of the scientists. You're going to have to help me."

"I know, it's just that—"

Sam nodded. "I have some very big shoes to fill here. Doctor Weir was very much loved and believe me, McKay has already reminded me about that about a dozen times already. She won't be forgotten."

"No," John agreed. "She won't."

"So what do you say?" Sam asked. "Truce?"

John sighed and nodded. All thoughts of giving Samantha Carter a piece of his mind were forgotten because everything that he had said she had touched on in one way or another. There was nothing that he could do about the current situation so he was damn sure to make sure that things ran as smoothly as possible. Elizabeth would expect nothing less. "Truce Colonel."

"Sheppard" Sam stated. "While military protocol demands that you call me by rank, while we're working together you're going to have to call me by my name."

"Samantha?"

Sam shook her head. "Sam's fine."

"Alright then," John agreed. "And Sam?"

"Yes Sheppard?"

"Congratulations."

"For what?" she asked curiously.

"For the promotion,"

Sam smiled. "Thanks."