TITLE: The War

AUTHOR: DramaLexy

SUMMARY: They may have won the battle, but the war has barely begun. Post "The Real World" Weir-centric with some Sparky-ness

DISCLAIMER: If they were mine… grins evilly

AUTHOR'S NOTE: I thought the end of the episode was just a little too neatly wrapped up. So I decided to continue the story. Enjoy!

Elizabeth's eyes were downcast as Carson finished giving her a final check-up before releasing her from the infirmary. He offered her a little smile. "You ready to get out of here, luv?" he gently asked.

She mirrored a much smaller version of his smile. "How could you tell?"

"My first advice would be to get some food in you. I'll come and check on you later this afternoon – I better not find you working in your office." She nodded. "All right, off you go, then."

Elizabeth looked across the room to where Sheppard was lying in a second quarantine area. "Is he going to be okay?" she asked Carson as she stood up.

"I believe so. I don't think the nanites – organic or not – have been able to override their initial programming to keep them from harming Ancients. The ATA gene protected him."

John caught her looking at him and gave her a little wave. She smiled in return. "I'm glad," she quietly told Beckett before leaving the infirmary.

Upon reaching the mess hall, Elizabeth realized she actually was starving. Even if her ordeal had only been a matter of hours, not days and weeks, that still meant she hadn't eaten all morning and afternoon. Once she'd gotten a tray, she saw Teyla and Ronon sitting at a table by the window. The Athosian waved her over to join them.

"How are you feeling?" she asked as Elizabeth sat down.

"All right, I guess…It's a little strange to be here after spending so much time getting convinced that Atlantis didn't exist."

"We're glad to have you back," Ronon told her. Elizabeth smiled.

"Thank you." A thought dawned on her. "If all of you have been in the infirmary all day, who's been running the city?"

Teyla smiled. "I was not downstairs all morning. Rest assured; Atlantis is not on the verge of sinking back into the ocean."

Elizabeth laughed slightly. "That's good to know."

"Dr. Weir," a voice called. As Elizabeth turned around, her eyes widened in shock as she found herself not in the mess hall, but in the common room of the mental hospital outside D.C. She closed her eyes, blocking out the image. "Dr. Weir?"

As she looked up, she saw Lieutenant Cadman approaching her table. She was back in Atlantis again, like nothing had ever happened. Everyone was looking at her a bit concernedly. "Y-yes?"

Cadman smiled. "I just wanted to say it's good to see you're doing better." She held up a file folder. "Should I give this to you or – "

"I will take it," Teyla told her. "Dr. Weir is not yet back on duty." Cadman nodded, handing her the report.

"Okay. I'll see you guys later, then." She headed off to get some food for herself.

"Are you all right?" Teyla asked Weir, noticing the look on her face.

"Y-yeah. I'm fine."

"It's good to have you back in the real world," Sheppard told Elizabeth as they stood together in the control room. She smiled.

"Thank you."

"Unless, of course, I've been infected by nanites, in which case – "

"John," she cut him off. "Don't." She knew this wasn't his artificial reality, but she still wasn't so sure that it was real for her. He'd been her beacon to guide her out of the confusion in her mind, and at that moment, she didn't think she had the strength to do the same for someone else.

"Sorry," he said a bit sheepishly, realizing his joke had been way off the mark. Not knowing if staying would make things better or if he'd open his mouth again and make them worse, he decided to move away, heading back downstairs.

Elizabeth was left standing alone on the balcony, staring down at the quiet Stargate and fingering her father's pocket watch. To tell the truth, she was tired, but was so desperately afraid of going to sleep. Would she still be on Atlantis when she awakened?

"I'll see you in the morning," she finally turned and told the officers on duty in the control room. They nodded to her in acknowledgement. However, she wasn't quite ready to go back to her room yet.

Out on the balcony, the sea breeze played with her hair, making it dance around her head. She hadn't worn it longer than shoulder length in years, but she liked it. The wind was also taking away the tears that slowly rolled down her face. Hardly anyone had ever seen her cry before, mainly just her mother. Helen Weir had been there to hold her the first time she'd had her heart broken by a boy, when the stress of her triple major in college had finally gotten to her, when her father had died, when she'd been in the hospital –

Elizabeth froze as she realized that the last event on that list hadn't happened. She hadn't seen her mother since she'd been home the previous year; her last trip to Earth had been too brief to even leave Cheyenne Mountain. Rationally, she knew it would take time to get past the day – weeks! – that she'd just experienced, but some part of her wished it would all just be erased. She didn't want to remember; how dare the replicators have done that to her?

She closed her eyes tightly as a sudden migraine came on, stumbling backwards away from the railing. The pain intensified, and the last thought Elizabeth had before succumbing to the darkness that overwhelmed her was that she hoped she would wake up.

Throughout her body, the nanites began replicating…