All recognisable characters are the intellectual property of people who I honestly can't be assed to look up. All rights are thus reserved, and this story may not be distributed on a profit making bases or without the authors express permission.
This story is a one-off and there will be no sequels, so don't bother asking.
Spoilers are as follow: to the end of Season 3 of Doctor Who and the first season of Torchwood, post season 10 of Stargate SG-1 and into season 4 of Stargate Atlantis (by which I mean the two episodes I have seen).
The armoury was full of solders and scientists, everyone who could hold a weapon being drafted in for one last ditch defence of the base. Major General Jack O'Neill, dressed in BDU's and full body armour walked through the room, checking the hastily assembled fire-team's equipment as he went. He had to shout to be heard over the sirens and near constant explosion that had already drowned out the sound of sporadic gunfire. Room shook in response to one particularly large explosion, a thin layer of dust floating down from the ceiling.
"That's everyone we could find, Sir." Lieutenant Colonel Cameron Mitchell came in and saluted, "We've lost contact with another two levels; I don't know how much longer we can hold out for."
"Any word from the Apollo?" O'Neill asked, unable to hide the desperate hope in his voice.
"Never stood a chance." Mitchell shook his head, "We don't know how, but they were intercepted long before they could get a shot off at the Valiant."
"Well, the Odyssey managed to take out the dry-docks before they left, and with the Daedalus already at Midway station, there's nothing that they can send after us." O'Neill looked round, "Okay, take as many men as you think you need and head back up. I'm going to see how the evacuation's going."
He made his way out into the corridor, fighting his way through the steam of refuges making their way towards the gate-room. They were the lucky ones; they had skills or knowledge that they either couldn't afford to lose, might need, or couldn't risk falling into the wrong hands. They were the ones with a first-class ticket to Atlantis, and hopefully, safety. Everyone else was considered expendable, and would be expected to hold the line, buying the time needed to get the others away with their lives.
"I need some good news, Danny." O'Neill climbed the stairs into the control room two at a time, "Tell me you've come up with a plan to stop them?"
"Wish I could." Dr Daniel Jackson shook his head, "It's all we can do to keep the Toclafane from phasing in."
"Okay, time to get moving." O'Neill looked round at the last few technicians, "Time to go, guys; nothing more you can do here. Grab what you can and head down to the gate: we'll take it from here."
"Request permission to stay, sir." Walter looked round, "I've been here from the beginning, and I'd kind of like to be here at the end."
"Okay, you can stay." O'Neill took a deep breath and closed his eyes for a moment, before grabbing his radio, "Mitchell, tell your people to start pulling back; almost everyone's through the gate."
"I'm afraid we can't do that, sir." The voice on the other end of the radio was half-hidden by static, making it sound like it was coming from far away, "We've had to fall back to the last checkpoint; they take this, they're be able to get to the gate-room."
"Then you know what I'm going to have to do." It was more of a statement than a question.
"It's okay, Sir." There was a moment of silence, "It has been the greatest honour of my life to serve with you. All of you."
"The honour has been ours." Daniel looked shaken, "Good luck, Cam."
"I ain't dead yet...look out!" There was a burst of gunfire, "Get out of here while you still can! I can't guarantee how long we can hold them for..." The radio went dead.
"GO! GO! GO!" O'Neill shouted, hustling the last few evacuees out the room as he grabbed his P90, making sure it was fully loaded before typing a series of alphanumeric codes into the base computer, activating the self-destruct program and scrambling the main computer. The sound of fighting grew closer and closer as they ran into the gate-room, huge dents appearing in the blast doors, as if some wild beast was trying to get through.
"That's everyone we're going to get." Jackson yelled, standing just in front of the Stargate.
"Thirty seconds!" O'Neill gave the room one last look as the thick metal doors finally gave way, allowing one of the attacking Toclafane through. The spherical entity hovered in the air for a moment, its many spikes and blades spinning round aggressively. The General raised his weapon and fired, the 5.7mm rounds just bouncing off the alien's exoskeleton.
"Jack!" Jackson grabbed his friend and pulled him through the event horizon.
To anyone still alive to witness it outside, it would have looked like Cheyenne Mountain was suddenly lit up by some internal light, then exploded violently, showering rock and flame all over the south west side of Colorado Springs.
O'Neill half stumbled, half fell down the ramp into the Midway Space Station, halfway between the Milky Way and Pegasus galaxies. He looked round, trying to compare the faces he saw to the people on the evacuation list. Several were missing, either killed by the Toclafane during their attack on NORAD and the SGC, or vaporised in the subsistent nuclear fireball that he had set in motion. He glanced out of one of the portholes and saw the welcome sight of the USAF Daedalus, waiting to destroy the station as soon as it was evacuated, thus effectively severing the link between the two galaxies.
"Sir!" Lieutenant Colonel John Sheppard made his way though the crowd and saluted, "What's going on, sir? The message we got was rather garbled."
"We have a foothold situation: Earth's been over-run by an unknown race called the Toclafane." O'Neill started towards the ladder that led up to the station's small control room, "It was all we could do to get off planet with as much equipment and as many people as we could." he paused for a second, "We lost the Apollo, but the Odyssey's on it's way, once they evacuate our off-world teams and pass the word around that Earth's under new management."
"How?" Sheppard followed closely, trying to get his head round what he'd just been told, "How in the hell did this happen?"
"I. Don't. Know." O'Neill stopped dead in his tracks, "The new British Prime Minister, Harald Saxon, announced the existence of extraterrestrial life, without the approval of the IOA, which called a conference on-board the Aircraft Carrier Valiant to discuss how to continue. We don't know what happened next, only that it appears that these Toclafane were working with Saxon, or he was working for them, but either way, they slaughtered the IOA council and Saxon declared himself Lord and Master of the planet, sending the Toclafane to kill one tenth of the population."
"Holy crap!" Sheppard blinked, "That go to be what, 600-million people?"
"For a start." The General looked round; the evacuees were already making their way through the other Stargate and on to Atlantis, "But we managed to get the Asgard database and all the information you guys have sent back from Atlantis off-planet. Whatever happens, they're not getting their hands on that."
"What about Earth?" Sheppard asked, "We can't just abandon everyone."
"What do you suggest we do?" O'Neill turned round, gesturing to the few survives, "We've lost the Apollo, almost all our resources and the SGC. The only thing we can do is make sure Atlantis is safe. Then at least we've got some place to fight back from." He put a hand on the other man's shoulder, "Trust me, we will be going home, someday."