Chapter 2

Her saying his name let a number of memories fall back into place. He'd tried to forget about her since the news of her death. It had devastated all of Atlantis to lose their leader, but had hit him the hardest of all, having lost the closest friend he cared a lot about. How much so he still wasn't sure, but looking up at her curly brown hair and wonderful green eyes, every feeling for her came rushing back. Happy, angry, worried, sad, all cascading down and encircling him.

He stood up, struggling a little since his hands were still tied behind his back, and continued to stare at her. Was it really his – their – Elizabeth, or just another copy?

She stood with her arms crossed, leaning with most of her weight on her left foot. She looked amused.

"Are you going to just stare at me, Colonel?" she asked.

John cast away his thoughts. "You're in charge of a replicator ship?!"

She looked downwards. "I'm still good, John."

He wasn't entirely sure about that, though he desperately wanted to believe it. "They told us you were dead." he spoke softly, voice heavy with emotion.

When he said this she looked up sharply, immediately realizing what he was thinking. "It's me. I'm half-replicator, taken by Oberoth in our mission to get a ZPM. But I escaped from him with a faction of Asurans."

John's eyes widened a little. The last time they had not given her her full memory. And why would Oberoth make a copy of her? It's really her, he thought. It's really my – our – Elizabeth. Though he wasn't entirely sure if it was a good thing as of that moment. At least there was hope now that they could bring her back home.

He had the urge to hug her, to touch her, but the look she now possessed stopped him.

"I'm glad you finally found us. I was beginning to get a little impatient. I was hoping you wouldn't just shoot us down. Sorry about your jumper, but I need your help."

He stared at Elizabeth somewhat disbelievingly. "You sat around here so we would come by so you could talk to us?""Yes. So?" She raised an eyebrow at him in the typical Elizabeth Weir fashion and he realized how much he missed that about her. Hell, he missed pretty much everything about her.

"'So?' Why'd you have to knock us out, blindfold us, and tie us up? Speaking of which, do you think you could untie my arms?"

She gave him a crooked smile. "Sorry John, I can't do that. And to answer your first question, well, I thought it'd be more fun."

"You thought it'd be more fun?"He gave her a look, a mixture of annoyance, disbelief, and amusement.

"Okay," he said slowly, drawing it out into two distinct syllables. "What do you need to talk about?"

Elizabeth became serious. "I need your help with a little project of mine."

"And what would that be?"

"Let's make a deal. I'll answer your questions after you answer a few of mine."

John hesitated. He wanted to know what Elizabeth was planning, but he also knew that he couldn't tell her anything important about Atlantis. "Ok." He finally said.

"Good. First one. I'm curious. Where's Teyla? I expected her to be in the jumper too."

"She's not on my team right now." He sounded slightly bitter.

She looked confused. "Why not?"

"Because she's pregnant."

Shock showed on Elizabeth's face for a brief moment before a soft, somewhat sad smile graced her lips. "Well you'll have to tell her congratulations for me.""Why? Are you going to let us go home?"

"Eventually. Who's the father?"

"Kanan."

"Athosian?" she guessed.

"Yes."Elizabeth thought she understood the bitterness now. She had always noticed a connection between Teyla and John. She figured that he must be jealous.

"Now," John continued. "My turn for a question."

"Wait. I've got more first. How is everyone else?"

"They're good."

"What about Keller? Is she head of medical staff?"

"Yeah. Doing a pretty good job, too. Between you and me, I think there's something between her and Ronon."

"Oh?"

"Yeah. Something definitely happened with them during that quarantine lockdown."

"Quarantine lockdown?"

"Yeah. I probably shouldn't have mentioned that."

"Who replaced me?"

"Colonel Samantha Carter."

Elizabeth grimaced, something that didn't escape John's attention. Though he noticed she didn't look particularly surprised that a military personnel was now in charge. "Don't like her?"

"Well, Colonel Carter and I didn't exactly see eye to eye when I worked at the SGC. How is she doing as leader?"

"She's doing a pretty good job." He admitted.

"Did you find a good planet to land Atlantis on?"

"Ye – es." He dragged out the word into two syllables, deciding that it was ok to tell her that small detail.

"How did you get rid of the replicators?"

John kept quiet and she sighed. She had known he probably wouldn't tell her that. "So who told you I was dead?" Her voice softened.

Pain appeared in his eyes but it was gone instantly. So instantly that Elizabeth wasn't actually sure if it had even been there. Then she couldn't read his expression at all.

"A group of replicators who made a fake Atlantis."

"A fake Atlantis?"

"Yeah. We came across another set of us. It was kinda creepy."

"So what did you do with my stuff?"

"We sent it all back to Earth. Your mother has it now." The pain was back in the eyes that matched her own and he had a faraway look on his face as if he was remembering something.

Flashback

John took a deep breath and rang the doorbell. A large cardboard box sat next to him on the front porch. The door to the small white house opened. A woman in her fifties was inside. She smiled but the smile disappeared a second later when she got a good look at him.

John knew she must be thinking the worst seeing him in his dress blues. Unfortunately, the woman was right to be thinking the worst.

Then the woman's eyes fell on the box. "Oh my God." Her hand flew to her mouth and tears started to form in her eyes.

"Mrs. Weir, I'm John Sheppard. I worked with Elizabeth." He had purposely left out his rank. The dress blues were bad enough. "Could I come in?"

Mrs. Weir didn't say anything. She just moved aside to let him pass. John picked up the box and stepped through the doorway. He was led to the family room, where he set the box down on the coffee table. She motioned him to take a seat on the couch while she sat across from him in an armchair.

John didn't know where to begin, but he didn't have to when she asked, "Is my daughter dead, Mr. Sheppard?" It was almost a whisper.

He had been trying to stay composed for Elizabeth's mother, but he knew some emotion was visible. "That's what we've been told, Mrs. Weir."

There was something in his tone thatmade her ask, "But you don't believe that?"

"I'm not sure. I don't want to."

"Can you tell me what happened?"

"I'm sorry, ma'am. It's classified."She just nodded and he knew that she hadn't really been expecting an answer. With trembling hands, Mrs. Weir reached into the box and pulled out one of the items in it. It was a silver pocket watch. The one that John had seen her holding several times – particularly after the time the nanites had invaded her body.

Elizabeth's mother stared at it for a few seconds before setting it down next to the box on the table. She then repeated the process with several more of Elizabeth's possessions. "You said you worked with Elizabeth?""Yes. She was my boss."An eyebrow lifted and John immediately knew where Elizabeth had inherited her expression from. "How was my daughter the boss of a military man?"

"Well, it is mainly a scientific expedition and they wanted a civilian in charge."

She nodded, not bothering to ask who 'they' was. "Elizabeth sent a few letters home during the last three years. She always mentioned you in them. Seemed like the two of you were close."The corners of John's lips curved upward in a small smile, despite his mood, upon hearing that Elizabeth had mentioned him in her letters to home. "Yeah. She was pretty much my best friend."From the look in his eyes, Mrs. Weir was pretty sure that he cared about her daughter as more, but didn't say anything. "Then I want to thank you for coming down here personally."

John was quiet. Then Mrs. Weir withdrew a ceramic pot from the box. She examined it for a minute. "I gave that to Elizabeth for her birthday." He told her.

"Then you should be the one to keep it." She placed it in front of him. "I know she would want you to have it."

He reached a hand forward and grabbed it. He held it, remembering that day. "Thank you."It was silent again for a few moments while she continued to look at all of Elizabeth's things. John finally stood up, saying, "Well, I should be going Mrs. Weir. I am truly sorry about Elizabeth."

She nodded and walked with him to the door. "Thank you for coming." He nodded too and then left.

End Flashback

Elizabeth didn't respond to his answer. So he took advantage of the silence. "My turn to ask questions now."

She sighed. "Alright, what would you like to know first?"

"Uh…how have you been doing? You know, in the last year.." Concern was clear in his voice as he trailed off a little awkwardly. This question wasn't quite the one she imagined would come first and she was touched by it.

"It was tough in the beginning," she admitted. "But I'm fine now."

"What do you mean 'it was rough in the beginning'," he demanded. "What did they do to you?"

"It doesn't matter." She avoided his eyes.

John was starting to get annoyed and frustrated. Sometimes during their conversation she seemed like the old Elizabeth Weir. The one he knew. But then at other times, she was unfamiliar to him – not telling him anything at all. He wasn't used to that from her.

"Of course it matters! What did they do to you?"

She didn't answer, staring off to her right.

"Elizabeth!"

She ignored him, clearly not wanting to talk about it. "Dolan, please take him back to the cell." She then turned away from him.

John felt two hands roughly grab him from behind. He didn't struggle and let himself be pushed out of the room. He was too busy thinking. He knew that Oberoth must have done something really horrible to her to make her react like that. And he wondered what it was.