I know I promised this a long time ago but I was having problems with this chapter and had no idea where I was going to go with it. So I hope you like it.

Sheppard closed his eyes, trying with all his might to escape but again nothing happened. He opened his eyes and glared at Atlantis.

"What have you done?" He growled. She took a step back and shook her head but said nothing, "What have you done?!" He shouted.

"I had to," She whispered, "To protect you."

"Let me out," He ordered forcefully. The kind of voice he used on his men.

"I can't," She stood her ground.

"Let me out of here!"

"I can't!" She repeated, shaking her head, "It is impossible."

"Why?" He took a step forward. She waved her hand over the water and the view of the chair room appeared. His eyes widened at the empty chair, "Where am I?" She waved her hand again and this time to a view of the infirmary. His body was lying in one of the beds, attached to various machines and his team sat around him. He crouched over image and reached out. He closed his eyes as the image faded away and his hand clenched, "Why is my body in the infirmary?"

"Your Doctor brought you there after the transplantation."

He shook his head in confusion, "Transplantation?" He questioned.

"When you sit in the chair your mind is temporarily connected to the computers. I have transplanted your consciousness into the computer….permanently."

"You did what?"

"You're mind can only be transplanted back if your body is in the chair and your friends believe you to be beyond help."

"I didn't ask for this!"

"Why can't you accept what I have done?"

"Because I don't belong here Atlantis. I'm needed out there!"

"I need you more!"

John stopped; he looked up at her, "What?" He asked softly as he slowly rose to his feet.

"We can be together now," She smiled and placed a hand on his arm.

He stepped away from her, "Atlantis," He said with a sigh, "I like you, I really do."

"But?"

"I like you as a friend Atlantis."

She shook her head, "I don't understand."

"I'm sorry, but I don't feel the same way. I thought you knew that."

She turned away from him. He took a step towards her, "I'm sorry," He placed a hand on her shoulder.

She shrugged him off, "Get away from me!" She cried.

"Atlantis, please."

"Leave me alone," She began to run.

"Atlantis wait!" He shouted.

"No!" She shouted back. She disappeared and Sheppard sunk to the ground. He dropped his head into his hands and breathed loudly.

"Atlantis," He said softly, "I know you can hear me……I'm sorry, I really am. But you have to let me go. My people need me, The Wraith are coming and I have to protect them, protect you from being destroyed." He received no answer, just the soft crying.

"I still want to be your friend Atlantis, I'll still visit, there's still so much we could learn from each other, but I have to go, I have to find a way out of here." He slumped back, lying over the water and watched the clouds in the sky. There was no wind, no smell of sea salt, no heat from the sun. He didn't know how he could ever stay there. He twisted onto his side and looked down at the rippling water and wished that he could sea his friends. His eyes widened as his wish was fulfilled and the water turned black and then back to the view of the infirmary where they were sitting at his bedside. He thought only Atlantis could manipulate the water. He concentrated and wished he could hear their voices.

"I'm so sorry lass," Sheppard recognised the Scottish accent, "I know how much you care for him."

Sheppard swallowed hard, "Thank you."

"There is something we have to talk about, How long we should keep him on life support. He wouldn't want to live like this." No! Sheppard thought. If they took him off life support then he would be stuck in the computers forever with no chance of getting back.

"I can't…not yet," He watched her shake her head and smiled. Thank god for Elizabeth, he thought. She'd just given him the chance he needed. If only he had a way of communicating with them. He frowned. If he could watch and listen to them, what else could he do. He thought about turning the lights on and off in the infirmary where his team was but wasn't going to risk it in case he accidentally turned the life support off instead.

A light bulb went off in his head and he thought about the Atlantian screen in Stargate operations. He pictured it in his head and typed a message. The water underneath him showed the message he was writing and he frowned at the Ancient symbols. Damn, the message was all in Ancient. Now he would have to wait until it was translated.

"Dr Weir?"

"Yes Chuck?" Elizabeth sighed into her radio.

"I'm sorry to disturb you but the screen's just popped up with a bunch of Ancient writing, I've already had Dr French to translate it."

Elizabeth frowned and tilted her head to one side, "What does it say?"

"In out, in out-"

"What is it? The lyrics to the hokey pokey?" McKay interrupted as he listened inover his own radio. Elizabeth sent him a glare.

Chuck continued, "Body outside, inside knowledge, Atlantis."

"That's all?"

"Yes Ma'am."

"Okay," He rubbed her temples, feeling a headache coming on. Her military commander and friend was currently being kept alive by machines and the last thing she needed was Atlantis sending cryptic messages. "Contact me if it happens again," She switched off and turned back to watch Sheppard sleep.

Sheppard sighed and mentally kicked himself. Of course his message wasn't going to translate word for word, The ancient language was a complicated one, one he'd never bothered to learn. Now he had to find another way to communicate with them.