Disclaimer: I don't own Stargate Atlantis or SG1

Note: Not beta'd so all mistakes are my own. Also as it appears that this needs to be stated. This Fic is AU, it takes place years into the future. Things have changed, people have change. Just because somebody wouldn't have done something back during season 2 Atlantis doesn't mean they won't do it 5 years into the future.
Pairing: John/Liz, Jack/Sam tension, Jack/Liz (Not quite sure in what context yet)
Spoilers: To be safe up to and including season 2 Atlantis and season 9 SG1

Darker Star

Cheyenne Mountain Complex (June 4th 2010)

Jack pulled a chair up to the infirmary bed and looked at the small fragile woman that was lying on it. He hadn't seen her in nearly 6 years but he could tell she'd been through the mill a few times. She had a black eye, a swollen cheek, 3 broken ribs one of which had punctured her lung and a sprained ankle. She was not looking her best. He placed his hand over hers and sighed. What had they done to her?

He heard someone enter the infirmary and he quickly moved his hand from hers. He looked and saw Sam walking towards them. She looked at Elizabeth, sighed then looked at Jack.

"How's she doing?"

Jack sighed. He knew Sam didn't care for Elizabeth but he also knew she wouldn't wish this on anyone.

"It looks bad and it is bad."

Sam sighed and sat next to Jack.

"I don't like her that much, but she shouldn't have had to go through this"

She looked at Jack and he was sure that, just for a second he could see a few tears form in her eyes before she quickly pushed them away. Jack cleared his throat and drew his gaze away from Elizabeth.

"How's Colonel Sheppard?"

Sam sighed.

"He's damaged more emotionally then physically. He's worried about Dr Weir, he wants to see her"

Jack nodded and stood up.

"I'll go and see him, will you stay with Weir? I don't want to leave her alone; if you don't want to I can get Daniel"

Sam nodded.

"It's okay, I'll stay here"

Jack smiled and left the infirmary without another word. Sam looked at Elizabeth and sighed, seeing her like this had really unsettled Jack and the worse thing was he didn't know what had happened. Nobody that had survived the expedition were up to talking and many of them were going to have trouble surviving through the night.
Only twenty came back, twenty of nearly 200.
Dr Beckett didn't make it, neither did Lt Ford. St Stackhouse didn't come back and neither did Dr Heightmeyer.
She sighed, apart from Elizabeth and John, Rodney had made it back, an alien name Teyla, St Bates and some more scientists and a few military.
When she saw them come through the 'Gate she was overcome by shock at their appearance and terrified when Elizabeth collapsed onto the ramp.

:Flashback:

Cheyenne Mountain Complex (June 3rd 2010)

The Stargate began to spin, the technician put the iris up, Sam, Jack, Daniel, Teal'c and Cameron entered the control room. Sam sat next to the technician and the Stargate engaged.

"Any IDC?"

Sam turned and looked at Jack.

"Not yet Sir"

The technician turned to Sam.

"Wait, we're receiving an IDC…It's Atlantis"

Jack began to walk down to the 'Gate room shouting over his shoulder at the same time.

"Open the iris"

Sam, Daniel, Teal'c and Cameron followed him down to the 'Gate room.

The iris opened and a few seconds later, someone walked down the ramp, followed by another and another. They were battered and bruised, their clothing was ripped, they were helping each other stand. Sam watched in shock as she saw a very dishevelled Rodney McKay walk through the 'Gate. She was expecting a smirk or something that was McKay but instead she could see he was broken, deep lines were around his eyes; he had a bruise on his cheek and was limping. This was not the man she knew.

Then she saw two men walk through supporting the small frame of a woman. She immediately identified the two men as Colonel John Sheppard and St Bates but she couldn't make out who the woman was, as the last of the people walked through John turned to Jack.

"Close the iris"

His voice was quiet, weak and broken; Jack shouted the order for the iris to be closed. The small woman who was being held by Bates and John suddenly fell from their arms onto the ramp. Jack quickly called a medical team as John fell to the woman's side.

"Elizabeth, Liz"

Sam froze as she heard John call Elizabeths' name. That was Elizabeth Weir. That small, fragile woman was Dr Elizabeth Weir. Sam snapped out of her trance and saw Jack rush over to the fallen Elizabeth and check her pulse. His gaze fell onto John as if assigning blame onto him. As the medical team entered Jack immediately lifted Elizabeth into his arms, put her on the nearest stretcher and ordered that she be looked at first. He then turned to John who was sat on the edge of the ramp breathing heavily; Jack softened and placed his hand on John's shoulder then helped him to his feet.

"Get yourself into the infirmary"

John nodded and followed the rest of his team out of the 'Gate room.

Jack watched him go and sighed. He ran his fingers through his hair and left the 'Gate room without a word to SG1. Cameron turned to Daniel.

"What the hell was that?"

Daniel turned to him, tears in his eyes.

"That was probably the last of our expedition team."

Daniel left the 'Gate room followed by Teal'c. Cameron and Sam shared a look before leaving the 'Gate room themselves.

:End of Flashback:

The door to the infirmary opened and Cameron Mitchell walked in and sat next to Sam in the seat that Jack had just vacated.

"How's she doing?"

Sam sighed.

"Not good"

Cameron nodded. He'd seen some horrific things during his time at the SGC but nothing like this. He couldn't remember Jack being as freaked as he was in the control room. Cameron looked at Elizabeth and instantly got the wrong idea.

"What went on between the General and her?"

He nodded towards Elizabeth and Sam shook her head.

"Nothing went on between them, why would you think that?"

Cameron shook his head,

"I just thought…you saw the way he reacted…it was…intense"

Sam shook her head.

"General O'Neill would be like that if it was anybody."

Cameron nodded and left his seat.

"I guess; it was just…that look in his eyes when she collapsed, he looked devastated"

Cameron left the room leaving Sam to contemplate what he'd just said. Sure Jack had been unsettled when he saw the team come through the Stargate and yes, he did seem very concerned about Elizabeths' wellbeing, but it was just professionalism, wasn't it?

TBC…

Do you want me to continue? Please no flames about killing off Ford, Beckett, Stackhouse and Heightmeyer. I've already flamed myself for doing that, but I had too.