Title: Waking Dreams
Author: Mer
Genre: General
Warnings: Character death, some violence, and a bit of coarse language
Season/Spoilers: season 1, vaguely season 2, but no spoilers, really
Summary: Elizabeth Weir relives a Genii invasion of Atlantis that resulted in tragedy. Plenty of Shep whumping. (character death, angst, John/Liz friendship)
Disclaimer: I don't own any of the characters. I'm just borrowing them for a bit.

AN: Thanks a TON for all the wonderful feedback I received here and other places for this fic! It inspired me to delve a bit deeper, in the form of a flashback. Oh, and there's WAY more whump ;) This is the first of three additional chapters I've planned.

Thanks again to Hah and Em for putting up with my constant pestering, for beta'ing, and for being Shep whump addicts ;)

- - - - -

Waking Dreams

By Mer

- Chapter 2 -

(flashback)

Dr. Elizabeth Weir rubbed her eyes. She was up late again, working on some reports to send back to the SGC. She didn't need to stay up this late to work on them, but she couldn't sleep anyways when one of her teams was overdue. She considered seeing what John was up to. He could be a night owl himself, and he, too, worried about their teams. Her thoughts were interrupted by a call over her radio.

"Dr. Weir? We've got an offworld activation."

"Is it Sgt. Stackhouse's team?"

"Yes, Ma'am. Just receiving his IDC now. He says they're doing fine."

Elizabeth sighed with relief. "Lower the shield."

- - - - -

In the control room, the two officers manning the gate received Dr. Weir's go-ahead and lowered the shield. They watched as Sgt. Stackhouse stepped through the gate, followed by three men in the grey uniforms of Atlantis. A moment after stepping through the gate, Stackhouse yelled up to the control room.

"Raise the shield! They're Gen-" A gunshot echoed through the gateroom and Stackhouse fell to the floor.

The three men opened fire on the control room officers and took them out before they could react and activate the shield.

"Commander," one of the men spoke into his radio, "phase one is complete. We're ready to bring in the rest of the troops."

- - - - -

Elizabeth was still in her office when she heard the gunshots. She put her ear piece back on.

"Col Sheppard, I'm hearing gunfire in the gateroom, I'm not sure what's going on down there."

"Stay where you are; I'm on my way. Elizabeth… stay safe."

Ignoring John's advice, she cautiously left her office and crept along the balcony, staying hidden below the railing. She looked across to the gate controls and gasped when she saw the two officers lying in front of the console. Elizabeth tried to make her way towards the fallen officers, but was quickly surrounded by armed men. They dragged her up by her arms and brought her over to the top of the gateroom staircase, where she came face to face with Commander Kolya.

"Dr. Weir," he smiled coldly.

A chill ran down her spine at the sight of the man, and her whole body tensed with fear. She tried to put on a brave face.

"What the hell do you want?"

Kolya addressed one of his officers. "Bring me Major Sheppard," he scowled, and turned back to Elizabeth. "He will pay for his crimes against the Genii people."

Elizabeth knew this man's ruthlessness and feared for John. She had called him here; if only she could warn him…

"He was defending his team and his city. You would have done the same thing in his position, and you know it!"

"Then you would be free to attempt to take your revenge against me, on behalf of your people, Dr. Weir."

Elizabeth glared. This man was hopeless. "What do you want with us? Surely your government wouldn't have sent all these men for your petty revenge."

"Isn't it obvious? We want this city, so we can better defend ourselves against the Wraith. You're not even of this galaxy - we have more claim to this place than you ever did. Now we choose to stake that claim."

She looked down into the Gateroom and saw bodies of fallen members of her team. How could they do this? They should have been allies against their common enemy. So many lives lost for this stupidity! She felt overcome by a wave of nausea and held onto the railing as her knees buckled. She clung to the hope that her team would find a way out of this. John always found a way.

She watched as more Genii soldiers emerged through the 'gate. Too many, she knew.

Her heart skipped a beat when she saw John being led into the control room by a team of Genii men. His hands were cuffed behind his back and his lip was bloodied and swollen, along with a red welt forming on his cheekbone.

"John!" she called out to him. "Are you ok? What did they do to you?"

"I'm fine," he shrugged it off. "We had a slight disagreement on the subject of handcuffs."

"How nice of you to join us, Major Sheppard," Kolya mocked.

"That's Lieutenant Colonel Sheppard now."

"Oh, well please accept my congratulations," his voice dripped with sarcasm, "short-lived though they may be. We have the city under our control now, with ten times the men we brought last time."

"Oh yeah, remind me of the score last time? Was it something like seventy to one?"

John said it to get under Kolya's skin, but she knew he didn't take any of those deaths lightly.

"Most of your men are already dead, Col. Sheppard, or they will be soon. I think I'll keep her for myself, though."

Elizabeth shuddered as Kolya put his hand around her arm, remembering his arm around her neck pulling her towards the 'gate, that day John had saved her life.

John seethed with rage and a desire to smack that grin off Kolya's smug face, but his hands were cuffed securely behind his back and two Genii soldiers held him in place. He settled for spitting in Kolya's face, a move that earned him a slap that nearly knocked him off his feet.

Elizabeth felt like she'd been struck too. How dare they? She couldn't stand to see John in pain and wanted to hold him, protocol be damned.

"Enough. Let's get on with it. Take him," Kolya ordered, and gestured with his gun.

The men obeyed Kolya's orders and roughly shoved John against the wall. He was surrounded by half a dozen Genii men, with guns aimed. How he maintained his veil of defiance and bravery she never knew; he was always strong like that. But at the same time he looked so small and vulnerable, and she wished she could stand by his side.

"What the hell are you doing?" Elizabeth demanded.

"As I said, Col. Sheppard must pay for all the Genii lives he took that day. All those men who never returned to their families."

"I had no choice!" If he had cared to see, Kolya would have seen the pain in John's eyes over those deaths. He hadn't wanted to kill those men, and never took a life casually; only to defend his own people. But blinded by rage, Kolya only saw a murderer of Genii.

"Neither do I." He lashed out and struck John across the face with the butt of his gun. John staggered backwards but didn't fall, as blood trickled down the side of his face.

"Stop this!" Elizabeth cried out, desperately.

"It seems Dr. Weir doesn't want to see you suffer. Would she prefer if we finished this quickly?" Kolya turned to her. "Your choice." He raised his gun to strike John again.

"Stop," she pleaded, knowing what her choice meant.

John groaned as his head was still spinning from the blow. "Kolya… You don't have to do this."

He was unmoved. "You put yourself in this position."

The two men locked eyes and John's glare was intense.

"I could have killed you!"

"Maybe you should have." Kolya aimed his gun.

Elizabeth tried to run to him. What was she going to do, throw herself in front of the bullet? They had plenty more where that came from. It didn't matter, she had to do something, anything. As she struggled against the rough hands that held her back, her eyes met with John's for one brief moment. One look that said so much: I'm sorry. Take care of each other. I regret… - She was almost free! - but it was too late. One shot. Then another, and another. Elizabeth watched as John crumpled to the floor and lay there, motionless. It hit her like a punch in the gut; she felt a wave of dizziness overtake her and gasped for air, willing herself to stand when her body wanted to collapse. At last she broke free of her captors, and this time they let her go because she was no longer a threat.

She ran over to her fallen friend and knelt beside him . "John," she placed a hand on his face. Get up, John. You always get up. You always come home. She put her hands on his chest in a hopeless attempt to stop the bleeding, but there was so much…

"Take her to the room over there and tie her up; we'll need her command codes," Kolya ordered.

Elizabeth felt strong hands jerk her up and pull her away from John. "No," she tried to resist. "No!" But she didn't have the strength to fight them. Kolya's men led her into her office and bound her hands to the arms of the chair, then left her there alone.

She'd never felt so alone in her life. When John was with her she'd always felt that somehow they'd pull through, even when all odds were against them. Now she was on her own, with nothing left of him but his blood on her hands.

Her solitude didn't last. She shivered involuntarily as Kolya approached and she strained at her bonds with the urge to violently attack the bastard.

He grinned hatefully. "Now, we're going to have a nice little chat about your command codes."

Elizabeth said nothing.

"You'd better start talking, or you'll end up like your dear Col. Sheppard over there… but it won't be so quick, for you."

"Go to hell." That was all she would say. She wouldn't give him the satisfaction of seeing her rage or her tears. She felt nothing but numbness now; he'd already cut her heart out, what else could he do to hurt her?

Kolya pulled out his knife and brought it close to her face. "You will give me those codes."

She didn't scream as Kolya plunged the knife into her arm.

- - - - -