A/N- 'BAMSR' was...oh how do I say it? Damn brilliant? Yes, it was damn brilliant. Not only did they bring back- or rather confirm that least an incarnation of our dear Lizzie is alive, but the replicators (or at least most of them) seem to be dead. All in all I'd call that a win...but how to incorporate Elizabeth into this episode, when a) she was already in it and b) I love the whole Elizabeth in control of the replicators thing... So, my canonically correct plot with Elizabeth in it may descend into AU 'cause I've got a bloody brilliant plot idea...which maybe I should for- nah. Never mind. 'Nuff rambling from the author- here's the next long awaited instalment of 'What Would Elizabeth Do?'

P.S- Slight spoilers for 'Ark of Truth' if anyone cares

Making a Choice

The briefing had not gone well and as Rodney stormed out both humiliated and furious Elizabeth could barely keep her anger in check. Especially when Ellis started spewing nonsense again, "I don't understand how you guys put up with..."

"Colonel," Elizabeth interrupted not able to keep it to herself anymore. "May I remind you that Dr. Rodney McKay is one of the most brilliant minds in two galaxies and that he has not only saved Atlantis from certain doom far too many times to count, but that he has also saved my own life on more than one occasion."

"I don't see your point."

Elizabeth glared at him. "The point Colonel is that Rodney may be the only one able to save us in the end. So I suggest that you simmer down, shut up and let the man do what he wants and not bait him nor humiliate him in front of his colleagues again because he is way smarter then you are."

"Dr. Weir-" Ellis began his disgust for Elizabeth well evident on his face. He hadn't liked it when Elizabeth was allowed to remain on Atlantis, he had thought that she was a security risk and didn't want to have anything to do with her but still- he had no choice.

"Colonel," Sam interrupted an equally evil glare on her face. "If you ever talk to someone under my command the same way that you talked to Rodney just now I will ensure that you will never be welcome back on this base ever again. Is that clear."

Taken aback by Sam's harsh words Ellis nodded. "Yes, it is."

"Good." Sam stated turning to look at John, Caldwell who had remained almost silent and Elizabeth. "We're done here, thank you."

They all filed out one by one with Elizabeth being last in line. "Hey Sam," Elizabeth stated as she was the last one in the room. "Can I say something?"

"What is it?" Sam asked with weary but open eyes.

Elizabeth smiled. "Thank you."

Sam nodded knowing full well what it was like to be in her position and Rodney's. "You're welcome."

-sparky-

Things were spiralling out of control. "You did what?" Elizabeth asked as she peered into Rodney's office. "Rodney, how could you?"

"Well uh- it was either this or nothing," he defended. "I know that-"

"No." She interrupted sternly. "I don't think that you do know. Colonel Carter is not going to like this and John..." she paused and chuckled with the irony. "...he is going to see this for what it is; a security risk."

"You know," Rodney began remarking with amazing clarity what he had been noticing for months. "You're becoming more like him."

"What?" Elizabeth asked fear clutching her heart as she wondered if Rodney had figured things out. "Like who?"

"Sheppard," Rodney remarked. "You've been seeing the military side of things since we rescued you and he well- he's become much more 'talk first and shoot second' which isn't like him..."

Elizabeth was caught off guard. "People change Rodney," she stated finally. "Look and me..." then with a smile she added; "...look at you."

That caught Rodney off guard and he had to agree with her. "Yes well uh-"

"Dr. Weir? McKay?" Carter's voice sounded stopping Rodney's sentence before he could really begin. "They're back."

-sparky-

"John?" Elizabeth asked catching up to John and Sam as they walked through the halls of Atlantis.

"Hey!" John stated his face lighting up, something that did not escape Carter's notice. She had heard through the rumour mill that she had disappeared into his quarters a couple weeks ago, just after the incident with the organic replicator clones and had not come out again till the next morning. Sam assumed that she should talk to them about it, but then she remembered that Elizabeth was just a member of the Atlantis expedition and therefore having any sort of intimate relationship with John was no different then Katie and Rodney getting together.

"I was just coming to see how it went." Elizabeth continued breaking off Sam's train of thought. "How many ships do we have?"

"Fourteen," John answered, his smile not diminishing as Elizabeth fell in step beside him. "Larrin said that she can get three or four more ships."

"Well that's great." Elizabeth exclaimed her heart lightening a bit- she had not liked the thought that her newly formed relationship with John would end just as it had begun on account of some stupid replicators. And yet, even as Elizabeth smiled in enthusiasm she could see that something was wrong. "John?" she asked, her concern evidence in her voice. "Are you okay?"

John was about to respond when Carter interrupted him her hand still on her radio. "John," Sam began, "Rodney wants to see us as soon as possible in my office."

"Just lemme have him for a couple minutes." Elizabeth stated, flashing Sam a smile that caused the new commander of Atlantis to nod, pushing down her own wave of jealousy as she heard Sam call the office her office. "So," she continued as Sam was out of earshot. "What's wrong?"

"I took Teyla off active duty."

This she had been expecting and thus wasn't surprised, but for John's sake she feigned innocence. "Why?"

"She's pregnant."

Elizabeth nodded as though she was shocked. "That would be a good reason." She smiled sympathetically and placed a comforting hand on his shoulder when suddenly he caught her eye and in that instant she knew that he knew.

"You knew!?" he whispered so as not to draw attention. "You knew and you didn't say anything to me?"

"It wasn't my secret to tell," Elizabeth explained her voice no more above a mere whisper. "What would you have me do?"

"I would have thought that my girlfriend would let me know when our mutual friend is putting herself at risk." John stated causing both himself and Elizabeth to stop for a moment at the word 'girlfriend' for they had never actually talked about their status, and John knew that now wasn't the time. "How long have you known?"

"Since the Athosians went missing," Elizabeth answered with a sigh while her mind tried to process why John had just skipped over the fact that he had called her his girlfriend. "She told me when I visited her that night in the infirmary. Listen I'm sorry but-"

John dismissed her apology with a wave of his hand. "Don't apologize, I know that you were in the right, and I was wrong to think that you should have told me," he flashed her one of his flyboy grins and then continued. "Come on, let's go see what McKay has done now."

Elizabeth groaned causing John to look at her. "You know?" he asked watching as Elizabeth didn't try to lie but merely nodded instead. "What do you know?"

"What he's done." Elizabeth answered taking his hand and leading him towards the control tower. "But I can't explain it- better leave that to Rodney."

-sparky-

"Does she know why she was created?" Elizabeth interjected looking at the image of the replicator on the screen. "I mean does she know what her purpose is?"

Rodney nodded. "Of course."

"Then she has a certain amount of self-awareness." Sam added.

"Yeah," Rodney agreed. "So?"

"So?" Sam asked cutting of Elizabeth before she even began. "Honestly I'm not sure how comfortable I am sending her to her death."

"Death?" Rodney asked himself in amazement. "It' can't die! It's not alive! It's a programme! I mean it's consciousness is just a bunch of ones and zeroes. I mean you can call it 'she' all you want but it's still just a thing. It's a prop- it's a really advanced radio-controlled weapon. I mean, you don't feel sorry for your bullets do you, your bombs?"

"Rodney?" Elizabeth asked sharply causing all eyes to fall on her. "She's alive, she's aware. That makes her more then a simple bomb or bullets. Those things have no intelligence, but that replicator there...why she's just like me."

"She is NOT just like you."

"Rodney," Elizabeth began again. "She is just like me. She has nanites keeping her alive, I have nanites keeping me alive. The only difference is that I am half organic- but even that isn't a difference. I have feelings and memories and we know first hand that the replicators have them too."

Rodney was becoming uncomfortable. "So what do you propose that we do?"

"I propose that we give her a choice." Elizabeth stated plainly hardly noticing that over the course of her rant that John had come to stand beside her. "I say that we let her know what it means to be human and then let her decide if she wants to take this mission on."

Sam nodded in agreement, "I agree with you Elizabeth but there's only one problem, what if she doesn't want to do it?"

Elizabeth looked from Rodney to Samantha and finally to John before turning her gaze back to the replicator on the screen. "Then I'll do it myself."

"WHAT?!?" Rodney and John nearly shrieked at the same time.

"No way," Rodney muttered.

"Damn straight no way," John agreed forcing Elizabeth to turn and look at him. "Why would you want to go on a suicide mission?"

Elizabeth smiled at him poignantly. "Why did you go on that suicide mission?" she asked watching a slight understanding come over John's face. "Because you had to," Elizabeth stated, saying what John was thinking. "And that's why I'll do it- because it has to be done...one of us needs to make a choice and if the replicator that Rodney's created doesn't want to then I will...the needs of the many out weigh the needs of the few."

"That's from Star Trek," John pointed out with a small smile.

"Doesn't mean that it's not true," Elizabeth said.

"Yeah well John's not Kirk and you are not Spock so don't give me that whole 'needs of the many' crap." Rodney stated angrily. "And besides it wouldn't work."

"Oh no?" Sam asked curiously. "Why not? Not that I'm saying that I approve Elizabeth but it doesn't hurt to have a plan b..." she smiled at the former leader of Atlantis and then turned her attention back to Rodney. "...so why won't it work? Elizabeth's nanites are the same as this replicators are aren't they."

"Strictly speaking..."

"Aren't they?"

Rodney sighed. "Of course they are and if I had to..."

"Well lets just hope that you don't have to." Elizabeth interrupted with a small smile. "Because believe me, I don't want to go anywhere." She turned to face John whose hands had dropped to her hands. "I have too much to live for."

-sparky-

Sam knew. How could she not know? She had seen the way that Elizabeth had looked at John and how she had reacted whenever he was in serious peril, but what she hadn't been expecting was that the second in command and the former leader would actually get together. And yet, the way that John and Elizabeth were arguing on the balcony made it all the more obvious.

Sam knew that with Fran agreeing to complete her mission that they wouldn't have to sacrifice Elizabeth- not that anyone was actually considering letting Elizabeth sneak into the replicator city and be the ticking time bomb- and yet Sam was still surprised that Elizabeth was arguing to go.

And as Sam watched John and Elizabeth argue she could see how their relationship had grown in the last couple weeks. To persuade her, John took Elizabeth's hands into his own, and put his hands lovingly on her face, Elizabeth in turn did the same and after a while Sam felt as through she had to walk away.

Making her way back to the office Sam wondered how they found the strength to be together. 'This galaxy is so full of peril,' she thought as she made her way through the final battle plans. 'anyone of them could die at any given moment...' Sam sighed and placed her pen down. '...but of course, being together makes all this time the more precious and more special, and that makes it all worthwhile. They are making a choice and sticking by it...'

There was a bitterness in her head that Sam didn't like having. For eight years she had pushed down the feelings for her own commanding officer and then when they were finally not in the same chain of command he would have nothing of it. And so Sam was left pining away for something that would never be... 'And then along came Cameron,' she smiled as she thought of the sparky young colonel who had reformed SG1 and pulled her along for the ride of her life.

'How I miss him...' and indeed Sam had grown incredibly close to Cameron and after they had saved their own galaxy from the Ori she had gathered enough courage to give him a slight kiss on the cheek. That kiss she had hoped would turn into something more, but giving the next crisis there hadn't been the time- and then of course, Atlantis had called and Sam like the willing solider she was followed.

"Colonel Carter?" Elizabeth asked standing in the doorway to her former office. "Sam?" she asked again causing the new leader of Atlantis to be broken out of her thoughts. "I uh- just thought you should know that Colonel Sheppard has managed to talk me out of joining the team on the mission."

Sam smiled. "Good. You'll be in charge of the city until we get back."

"I'd like nothing better."

-sparky-

"Welcome back," Elizabeth stated with a broad smile as John was beamed down onto the inner balcony of Atlantis over looking the gate. "It's good to have you home."

"It's good to be home." John stated with a cheeky smile turning from Elizabeth to Rodney who was busy on a computer. "How goes our good friends the Wraith?"

Rodney could do nothing but sigh. "They never showed up at the rendezvous point and I doubt that they could have gotten caught in the explosion. The most rational answer is that they knew that there was nothing left for us to talk about so they just went along their merry way and we're back to being enemies."

Elizabeth sighed. "Back to being enemies with the wraith, the replicators don't exist anymore... can we count this as a win?"

"Oh yes," John agreed. "We can defiantly take this as a win."

"Oh yes, all is right in the world," Rodney stated with a roll of his eyes. "-and speaking in being right with the world I've just deleted the replicator home world from our database which was actually a lot harder then one would have thought."

"M7R-227 you were a complete pain in the ass," Elizabeth stated with a smile as the light on the screen designating the planet disappeared into oblivion. "It is so good to see you go."

John sighed. "If only it had been this easy."

"Mmm," Rodney agreed closing his laptop. "Area 51's working on it."

Elizabeth smiled. "That's good to know," she turned to face John. "Do you wanna get a late dinner?"

"Absolutely."

"Can I come?" Rodney asked watching as Elizabeth and John turned to leave together. "To uh- eat dinner with you guys?"

"Sorry Rodney," John apologized looking over his shoulder. "But this is a dinner for two."

"Stupid lovebirds..." Rodney muttered under his breath as John and Elizabeth left the control room hand in hand. "Stupid, stupid lovebirds."