Title: Waking Dreams
Author: Mer
Genre: General
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: As promised, the sad stuff is over and now it's time for a more lighthearted ending (but not completely so). It got a bit long again, so there's one more chapter to go after this one (she says, for the fifth time...). If you prefer depressing endings, stop reading here :P Thanks again for your great reviews, and to Hah, Em and Beanie for the help!

- - - - -

Waking Dreams

By Mer

- Chapter 5 -

At first, his world was chaos. He struggled to find his place in it, to create some semblance of order. A concept formed in his mind and he grasped for it: identity? His mind grew clearer; I'm John Sheppard. From Earth. No… from Atlantis? Thoughts of those places made him aware of his surroundings, but when he tried to take in the vastness and silence around him he was quickly overwhelmed. Lost. Alone. Where am I?

The transition can be difficult. You must give it time, John. A voice spoke to him, but he couldn't identify the source. He felt a presence emerging from the silence.

Transition? Memories flooded back to him. Kolya with a gun pointed at him. Elizabeth's eyes full of panic and tears…he wanted to reach out, to say something to her… Gunshots. Searing pain in his chest… he gasped for air but there was only pain…then darkness.

I died?

He tried to let the strange idea sink in. This wasn't what he expected death to be like. To be honest, he had expected nothing; just a darkness that he would never awake from. This was…different. He wasn't quite sure what this was, but there were other concerns pushing to the front of his mind.

What happened to the others? My friends?

As if in response to his thoughts, the emptiness fell away and he saw Atlantis; not exactly how he'd seen it in life, but it was there. He could feel the people inside – his friends, the Genii – their fear, their pain… Then there was a flash of light and he could feel it as if he was a part of the city, as it was dying. Everyone he had known, his home, the knowledge of the Ancients, it was all destroyed in an instant. He would have stopped it, but he didn't yet know the power he had to reach out with his mind. All he could do was watch, and grieve. Elizabeth…

He felt the presence grow stronger around him until he was at last able to put a name to it. Chaya?

Yes, John. Don't be afraid, you're safe here.

What about Atlantis? You could have helped them. You could have saved all those people!

You know that is not true. You know the rules, we cannot interfere with corporeal matters.

You didn't seem to mind interfering with me.

John…

So, he was ascended now; on a higher plane of existence. His friends were gone, Elizabeth was… It was too much for him to grasp all at once. He sure didn't feel more enlightened.

Why did you bring me here? If all I can do is watch, you should've let me die with the rest of my friends.

Not everyone was lost…

John followed Chaya's thoughts to an object in space. He searched his corporeal memories; a puddlejumper. There were survivors! He let his mind take him towards the jumper; it almost reminded him of flying one. This part, he thought, he could get used to. He took himself inside the ship and felt joy and relief wash over him when he saw Elizabeth there, with Carson and Rodney at her side. John watched her tear-stained face and felt the grief radiate from her and encircle him. It pained him to see her like this and he felt responsible; he wanted to reach out to her, to comfort her any way he could. John imagined himself raising his hand to touch Elizabeth's face and she lifted up her head. Elizabeth, it's me. I'm okay. You're going to be okay. For a moment he thought she was looking up at him, but she turned away and her face fell into the same blank expression.

Frustrated, he sought out Chaya again. Please, send me back. I know you can do that.

John, I can't do that until you have at least experienced more and considered what we have to offer you. You cannot imagine the wonders of this universe… Please, at least give it more thought before you decide.

He admitted to himself it was worth more thought. He longed to return to comfort Elizabeth, but what would she say about his giving up this opportunity so hastily? He'd always admired her spirit of exploration and found it had rubbed off on him more than he'd realised. The knowledge he could acquire could have immeasurable benefits, and those non-interference rules – well, rules could always be bent, couldn't they? The rest of the survivors of his team would take care of Elizabeth; that's what they did. That's what they'd always done. Feeling more resolved, John set a destination in his mind and let himself soar.

------------------------------------------------------------------------------

(Six months later)

The passage of time in the world of the ascended is not like that of the corporeal world; it's fluid in nature, not precisely measured, and largely ignored. So it was that John Sheppard returned to Earth, unaware of the months that had passed since his death. Home, he thought, and wondered if there was still any meaning attached to the word. Strange as it sounded, he'd never felt truly at home until he'd arrived in Atlantis, and there was no going back there…

Once you have crossed over, you cannot return. Are you certain of your choice?

Yes.

You may choose the place in which to retake your human form.

John let his home world draw him in. From the static noise of billions of souls, he focused on the one that pulled at him with the most force. With one single thought in mind, he let himself fall, towards home, into darkness. Elizabeth…

- - - -

Elizabeth was up late reading, again. She still had trouble sleeping, six months later.

Dressed in an immaculate black pantsuit, she stepped behind the podium. She didn't usually dread public speaking, but it was different this time. She didn't want to speak the words that would make it final, she wasn't ready to let go. Elizabeth cleared her throat. "Lt. Col. John Sheppard" - she paused as the words stuck in her throat - "was the heart of the Atlantis mission."

Six months since she'd been in front of the crowd at the memorial service, speaking her public goodbyes to everyone she'd lost; she was still working on the private ones. Though it didn't seem fair to the others, her thoughts usually dwelt on John. Of all the team members she'd grown close to, she'd cared for him the most; more than she'd allowed herself to admit, until he was gone. Of all the deaths she'd witnessed that day, she felt most responsible for his. The events played over and over in her mind – questioning every decision, wondering what she could have done to save him; wondering when she would be able to close her eyes without being tormented by the image of John's lifeless body. The only thoughts powerful enough to repress those images were her most vivid memories of John in life: bright smile and quick wit, never failing to make her smile in return; unwavering strength and selfless courage, comforting her in their darkest hours; hazel green eyes that betrayed the intelligence and emotion he kept carefully hidden below the surface. Though she had been physically attracted to him from the beginning – he was a beautiful man, she admitted – there was so much more to John than met the eye, and she felt she'd only begun to scratch the surface. They'd kept their distance for professional reasons, the right thing to do at the time, but now she was left only with regrets and haunted by what-ifs.

Elizabeth realised that she had been staring at the same page for twenty minutes, and put the book down with a sigh. She got up and wandered to the kitchen to distract herself from her thoughts.

- - - -

John slowly opened his eyes as the universe spun around him, trying to sort out where exactly his place was in it. Shaking off the strange feeling of disorientation, he blinked and tried to move his limbs. Two arms, ten fingers…he looked down…clothing? That's a negative. At least all his important parts were accounted for. He tried to sit up and smacked his head against something hard and metallic. Ow. Pain. He hadn't missed that corporeal feeling.

- - - -

Elizabeth jumped when she heard a noise coming from her bathroom. Not just a noise, but the voice of an intruder in her home. After a moment of panic, she remembered the training she'd had with Teyla during her time on Atlantis and grabbed the nearest object she could brandish as a weapon. Courage gathered, she prepared to face the intruder with a rather large stainless steel pepper grinder in hand. She crept down the hallway and paused outside the bathroom door, taking a deep breath before she flipped on the lights. Instinctively she jumped back and took refuge in the hallway as an equally startled man hid behind her shower curtain. Temporarily blinded by the bright light, she hadn't been able to see much more than the figure of a man in her bathtub. She was pretty sure he wasn't wearing any clothing. Great, she thought. Probably recently escaped from the mental institute. Elizabeth briefly considered dialing the police, but for some reason felt drawn back into the room instead.

"Who's in there?" she called out cautiously, and added, "I'm armed."

A pair of eyes and a mess of hair peeked around the edge of the curtain.

"What are you going to do, sprinkle pepper on me 'til I sneeze into submission?"

Her guard dropped and her voice softened with tearful awe. "John?"

Elizabeth wondered if her own sanity should be in question as the man that looked like John – her John – reached out for a nearby towel, wrapped it around his waist, and stepped out from behind the curtain. But right now she didn't care if this was a dream, or a hallucination; she ran over and clung to the illusion. He felt real, and whole.

"Elizabeth." This time he hugged her back, and she was shaking as he wrapped his arms around her.

"How…? Is it really you…?" She was overwhelmed with questions, emotions, doubts… She wondered when she would awake from this dream.

"It's me…" A puzzled look crept over his face. "I'm not… quite sure what happened… I think… I died?"

The memories Elizabeth had been carefully pushing away flooded back upon hearing John's words and tried to fight the tears that were forming in her eyes. John saw the pain in her eyes and knew that what he said was true. He tried to reconcile the memories of his life before and his life now.What had happened to him? There was a piece of the puzzle missing, floating on the edge of his consciousness, just out of reach. Right now all that mattered was Elizabeth needed his comfort, and he let her tears fall on his shoulder as he held her close.

In his need to hold Elizabeth, John had forgotten his need to hold up the towel, which chose this moment to drop in a pile around his feet.

His eyes shot open as his face flushed with embarrassment. "…This is kind of awkward."

"Mm-hmm," Elizabeth mumbled in reply, oblivious and wrapped up in the comfort of the embrace.

"Do you..uh.. have anything I could wear?"

"Wear?" She looked up at him. "Oh…" Then she looked down. "Oh!" She, too, began to blush and spun around to grab a nearby bathrobe for him. Trying to avert her eyes for the sake of his modesty, she couldn't help but admire his slim, muscular form which she'd never been able to fully appreciate before. John took the robe from her and gave her a little grin while he wrapped himself up in it, as though he knew what she'd been thinking.

Elizabeth led him away from the bathroom and into her living room where they could sit and talk more comfortably. She watched him as he sat and wondered what was going through his mind, beneath his unreadable expression.

"John, what do you remember?"

He looked down at his hands while he contemplated for a minute. "I remember my life before… I remember the Genii, and Kolya…" Elizabeth saw shock and anguish flash in his eyes as the memories of that terrible day returned to him. "I… I wanted to reach out to you, but I was falling… into darkness… then, there was so much confusion, emptiness… and a voice… Chaya."

"Chaya?" She knew John had a connection with the ascended Ancient, and his genes made him closer to an Ancient than anyone else on the expedition…Was it possible? Had he ascended? She could think of no other explanation, and besides, she had heard about Dr. Jackson's ascension.

"John, you ascended?" Her voice was full of awe, and curiosity.

A floodgate in his mind opened and John closed his eyes as memories rushed back to him at a dizzying pace. "Woah." He blinked."That was…weird."

"John, are you okay? What did you remember?"

His eyes were wide with shock and darkened by grief. "Everything."

- - - - -