Title: Waking Dreams
Author: Mer
Genre: General, action/adventure
Warnings: Character death, some violence, a few naughty words
Season/Spoilers: season 1, vaguely season 2, but no spoilers, really
Summary: Kolya and the Genii return to Atlantis in force, seeking revenge and control of the city. Plenty of Shep whumping. (John/Liz friendship, angst)
Disclaimer: I don't own any of the characters. I'm just borrowing them for a bit.

AN: Many thanks for all the reviews on my last chapter! And a huge round of applause for Hah and Em for ALL the help they've given me :D I'd also like to blame them for this chapter getting so long I had to split it into two parts, so now there are actually two more chapters coming ;) But the next one is nearly finished so I should have it up soon.

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Waking Dreams

By Mer

- Chapter 3 -

(flashback continued)

Blood, there was so much… John's blood. Elizabeth watched it saturate the sleeve of her jacket, but her hands were tied and she couldn't stop it; she couldn't save him. The pain brought her back to reality as her numbness lapsed momentarily. No, it was her blood this time…

Kolya was growing frustrated. "We're already in control of the city, Dr. Weir. There is no need for your defiance."

For John, she thought. For all those who died today. She wasn't going to give in to him.

Kolya struck her across the face and sent the room spinning. "Luckily we have all the time we'll need this time. You'll break eventually."

A voice crackled over his radio and he walked away so Elizabeth couldn't make out much of what was being said.

"Excellent," he spoke into the radio. "No, I want him alive. Bring him to the control room."

He smirked and turned back to Elizabeth. "I think this might help convince you."

She heard him before she saw him. "…I don't have time for this, there are people out there who need my help, now – Elizabeth!"

"Carson!" Her first thoughts were relief that he was alive and unhurt, but she knew this was not going to be good.

"My God, what did they do to you?" Carson tried to move towards her but he was held back. "She needs medical attention, let me go to her!"

"That'll be the least of your concerns soon." Kolya pointed his gun at Carson and turned back to Elizabeth. "How brave are you going to be when it's not just your life at risk, hm? The command codes, or he dies."

No, she couldn't go through this again. John had been military, he'd known the risks… but Carson, he'd had no idea what he was getting into. She saw the fear in his eyes. Fake codes, give him fake codes, she though. But that would only delay Kolya for a few minutes and anger him further.

"It's okay, Elizabeth. Don't tell them anything."

"Time's up. Last chance to save your friend, Dr. Weir." She watched him squeeze his finger on the trigger and shut her eyes as she heard a gunshot.

She kept her eyes squeezed shut, not wanting to face the reality, when more gunfire and shouting erupted around her. When she finally opened her eyes, Kolya lay on the floor and a very shocked and frightened Carson was still standing. Major Lorne stood in the doorway, P90 raised. He turned to the two marines with him and ordered them to secure the control room entrance.

"Dr. Weir, let's get you out of here. Are you okay, Ma'am?" he asked as he unbound her wrists.

"Yea, it's nothing…" she replied, still in a state of shock.

"I'll be the judge of that," Carson interrupted, and hurried over to examine her.

Lorne took a field bandage from a pouch on his vest and handed it to Carson. "We've gotta get out of here now. There'll be more Genii here any minute."

Elizabeth stood up slowly as Carson quickly wrapped the bandage around her injured arm. She looked down at Kolya on the floor and it gave her a small relief to see him lying there. She gasped as his eyes shot open and he stared directly at her as he spoke, barely a whisper.

"This…won't make a difference… You've already…lost."

"The control room is secure, let's get moving. Dr. Weir, you know how to use one of these?" Lorne walked over and handed her his Beretta pistol.

Elizabeth took the weapon in her hand. John had taught her how to shoot after her last encounter with Kolya because he thought it would help her feel safe again. She'd agreed because it comforted him - knowing she could protect herself - but she'd never imagined actually taking up a weapon like this. Kolya was still spouting arrogant threats and every time she looked at him she relived John's death. Elizabeth found herself raising her weapon, driven only by her fury that overpowered her natural aversion to violence; she'd deal with the consequences later. She flipped the safety off with her thumb and fired at her target until Lorne put his hand on her shoulder. Kolya didn't speak again.

Lorne stared. "I'll take that as a yes."

Carson's mouth hung open in shock.

"What's our status, Major?" Elizabeth questioned, her face now calm and void of emotion.

"All of the inhabited areas of the city are under Genii control. We've rounded up all the survivors we can find and we're bringing them to the jumper bay. I'm afraid there's nothing more we can do." He paused for a moment. "Dr. Weir, we can't let them take the city."

She knew what he was asking of her. She nodded and let him lead her towards the control console.

Destroy the city. Elizabeth knew this was a decision she'd regret for the rest of her life, but what choice did she have? Lorne was right - letting the city fall to the Genii was as bad as letting it fall to the Wraith. They'd give the Wraith the location of Earth in an instant to save their own asses. But to lose this vastness of Ancient knowledge and technology over stupid human pettiness made it hurt even more.

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As they walked towards the control panel, Elizabeth fought the urge to turn around and run; run somewhere far from this place and everything that had happened here. She wasn't ready to face what lay near the control console, the friend she had failed - but they needed two command codes to get the job done. There was so much at stake here – Earth, the Milky Way – she had to push her emotions aside and get on with it. She'd done it many times before in negotiations, she could do it once more.

But when she saw him lying there, her carefully built resolve crumbled and she froze, the room spinning around her. I can't do this. This wasn't the John she remembered. He looked pale, and broken; surrounded by blood.

"My God," Carson spoke softly, and ran over to John.

Elizabeth followed him and they knelt beside the body of their friend as Carson checked for a pulse. "Can you do anything for him?" she asked with a faint hope, though in her heart she knew the answer.

"I'm sorry." Carson's expression was grim, and she knew this had hit him hard too. He took Elizabeth's hands in his, and she felt a small comfort in this simple gesture which connected her to life when her mind was filled with death. He stood up a moment later and placed a caring hand on her shoulder before going to check for survivors in the control room. Elizabeth stayed beside John's still form and brushed her hand through his hair. We will take care of each other.

"Dr. Weir? I've input my codes. We need yours right away so we can get out of here before more Genii show up."

"Yes, of course." She blinked away the tears that were threatening to form in her eyes. She couldn't cry, not now. Command codes. Concentrate. Tears would be acknowledging what had happened and she couldn't afford to do that yet or she'd shut down completely. Focus on your goal. She typed in her code and held her breath as she hit the button to confirm. God, what had she done? They were losing so much…

The countdown flashed onto the screen. Twenty minutes to get out.

Carson returned and reported no other survivors in the control room.

"Alright, let's get moving. We've got twenty minutes to get to the jumper bay and get the hell out of the blast radius."

"Wait," Elizabeth put her hand on his arm. "We can't just leave John here!"

Lorne's expression softened. "I'm sorry ma'am, we just don't have the time and can't afford the extra burden. We've had to leave everyone where they fell…" She looked at him and saw the pain of loss in his eyes too. He lifted up her hand and she felt something cold against her palm; a moment later Major Lorne's stern military façade snapped back into place and he turned away. Elizabeth looked into her hand and grasped onto John's dog tag like it was all she had left in the world.

"We've got Genii on the way!" one of the marines guarding the door reported.

"Let's move!" Lorne ordered, and gestured for Elizabeth and Carson to follow the marines.

She took one last look at the gateroom and her fallen friend. Goodbye, Atlantis. Goodbye, John.

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