Summary: Giftfic for anuna_81. Sometime in an AU s4, Atlantis is invaded and then it gets some very special help
Rating: PG13 - lotsa John!whump
Disclaimer: I ain't got no money, and nobody'd be daft enough to pay me for this. As it is thought, so let it be said; you make the toys, I play with 'em.

AN: many thanks to the friends that lent eyes and expertise and encouragement!

Chapter one

It was amazing how fast things could go to hell, John thought. As he lay on the cold floor, feeling himself slowly bleed to death, he couldn't stop going over the steps that had taken an ordinary day, and led it to the end of his people, his city.

Six hours ago an unknown ship had arrived in orbit and started bombarding the shielded city without warning. The energy weapons the newcomers used began draining the shield immediately, and their own weapons didn't seem to have any effect, either Human or Ancient. With a chill of premonition, John had ordered the evacuation of non-essential personnel to the Alpha site. Which was just as well because they had no time to dial the gate to get anyone out when the shield suddenly dropped below its ability to keep the enemy from beaming in.

Unable to hold the too-open gateroom under the ground-attack, John had shot up the terminals as he and Ronon covered the retreat of the scientists back into the corridors, hoping that that would be enough to keep these damned advanced aliens from making use of the gate.

Who they were, where they came from and why the hell they decided to attack Atlantis, were all questions he'd had no time for, though how the makers of Predator could have come up with something so eerily close.. was as annoying to think of as naked little green men beaming bombs around from the deck of an Earth starship. The enemy fell to bullets, which was good; except that at least some of them had personal shields. Not to mention that some of their weapons punched through Atlantean walls like so much butter.

All of which was a far cry from the annoying but boring diplomatic mission he'd been doing last-minute reading up for this morning.

Trying to make his arm move as his back chilled and his thoughts slowed, John remembered how he'd been missing being in the field. From the time he and the boys had gotten their pilfered ZPM back to Atlantis and finally met up with the Apollo at their new home, he'd felt the responsibility for the soldiers and scientist that called the city home shackling him, tying him down to the paperwork, and to every wall and terminal of the city itself. He'd barely registered the shock when General O'Neill showed up and told him he was officially in command. His mind had been focused on fixing his damaged city; on who was dead, who was injured and who could fill their duties.

That focus had allowed the volcano of pain and guilt he was feeling to stay buried until it could crust over and whet into the rest of the regret that he lived alongside. When he finally rose out of the daze, he'd found himself in Elizabeth's -even in physical agony, the name and all the emotions it carried through him made him wince-. In Elizabeth's office. In her spot watching teams walk through the gate -into danger or returning victorious. Paying an attention to Rodney and the other scientists that John-the-soldier couldn't be bothered to attempt. John-the-administrator did everything he could to watch over Atlantis for the lost, waiting for the day when he could hand it back to its true keeper.

It was almost stranger to notice how his team had changed with him, taking on new responsibilities rather than trying to go on with a different team leader. Ronon had officially taken over training; from doc Heightmeyer to the most experienced marine, everyone learned how to fight off any attack and how to survive in the field -to Ronon's satisfaction, not to mere Air force requirements. Teyla had taken on even more of the day-to-day administration, filtering how much ended up in John's hands. And Rodney, Rodney spent more time doing research and actually leading the other scientist, slowly being taught by Teyla to get along with them enough to be an efficient leader in his own right.

It hadn't taken the men's tempers or Teyla's uncharacteristically sad silences for them all to know they weren't where they wanted to be. That they were settling for what was necessary. Even more so than usual.

As the weeks passed, John accepted that they weren't going to get their old life back; at least not soon. He continued to hope; would *always* hope, thanks to all the other wonders he'd seen. But he realized he couldn't survive if he was constantly waiting for his life to right itself; he had to accept that *this* was his life for now. He could not treat it as settling, lest he shortchange the people who trusted him to lead them. Shortchange *her* memory. It was a slow process, but he adjusted, taught himself to eat enough to be healthy, sleep enough to think straight. Ignore the pain that stabbed through every time a team returned without news of their leader or the IOA made some passing remark.

As the months started rolling by, Teyla was even teaching him to be a smoother negotiator; which was a good thing, since she had promised her dreadlocked husband to stop going through the gate at the end of her first trimester.

A bit of research before any meeting was one of her first lessons; know the culture - avoid the foolish potholes. Boring. Not as bad as listening to scientists rave about Ancient contraceptive techniques and manufacturing technology, but still the kind of inactive activity that made him *yearn* for the days of running through forests with an angry mob on his tail.

But fending off an attack within Atlantis itself was an entirely different story.

----

Running through the corridors from lab to lab, escorting Rodney and Zelenka, wunderkinds extraordinaire, as they scrambled to make a better alien trap, John was glad for the link his friend had helped him improve with Atlantis.

An evening of John touching Ancient widgets while the scientist explained the latest projects needing funding had gone quiet when they didn't have any more work to discuss; the ever-present grief and guilt that rose between them choked any chance at their old teasing. When John's twitching fingers had activated yet another workstation panel, Rodney had tried for an idle tone as he mentioned some sub-routines he'd found that he thought might be related to communicating with holders of the Ancient gene.

John knew he had to do something to maintain his friendships, however much he couldn't find it in himself to be his old cheerful self; yet. So he agreed. And when Atlantis started having more of a personality, started actually communicating with him -albeit like a toddler-, John realized that not only did it give them a hell of an advantage in figuring out the secrets of the Ancients, it could mean victory in a battle.

Or so he'd thought. Being able to control the doors of the city was of limited use when some of the bad guys could melt through them. Still, they at least had a way of tracking the invaders and knowing how they reacted to any new wunderkind action, not to mention tracking the other teams also hiding on Atlantis; also trying to beat off the invasion.

Until suddenly the connection was gone. For no apparent reason, Atlantis was gone from his mind. Not even the vague impressions of his early days in the Pegasus galaxy. It didn't take one of the geniuses to tell him this was *not* good. Advanced aliens that couldn't be stopped and a computer system that no longer talked to them; it was pretty basic math.

It didn't change what had to be done though. It was just another casualty; another of his 'people' lost. Of course, like any key player, Atlantis' loss hastened the end; they couldn't track the enemy any more, and then the Ancient terminals started shutting down and refusing commands. A huge *leap* into Hell.

Down to using their laptops to try to come up with some wild plan, and constantly trying to avoid dodge patrols, John had split the team, not speaking the thought that it would double their enemies' targets. At this point, that hardly seemed enough to give any of them any particular chance at survival, but it was all he had to offer. As he watched Ronon shove Zelenka through a door that started to close for no apparent reason, he wished them godspeed and dragged Rodney in the opposite direction, getting a chill from the sudden flicker of the lights. The creak of materials under stress was getting louder, humming through the floors and walls. Something was happening to the city; something worse than shutting out the remnants of the expedition.

Another hour on the run and Rodney was hit, a chunk taken out of his leg by some weapon that shot a wide beam of energy. John got the bad guys and dragged his buddy into a room, furious that he couldn't at least make Atlantis close the door behind him.

"Rodney-" John's voice choked, his hands shaking as he automatically reached for the med kit he wasn't carrying, his eyes fixed on the bloody dent in the other man's leg. If the ray gun hadn't seared the flesh as it passed through, it would already be too late.

"Forget it." Rodney was breathless and speaking through clenched teeth, clutching his laptop with fingers as white as his face. His head jerked to the side, wide eyes fixed on a bank of low cupboards. "There."

John followed the gaze, hoping for a miracle.

"Get me in one of those and then get out."

"Rodney-"

"There's at least a chance they won't find me," The scientist gave John a grim look, "If I can think of a way to get into the computers and access the damned self-destruct..."

They stared at each other in silence, not needing to admit that they'd given up the hope of winning. They just didn't have a choice but to keep fighting until their last breath; surrender to people who had not even tried to communicate before attacking.. seemed beyond futile. Rodney had been around military types too long; fighting to the end had overrun his native cowardice a long time ago.

John had finally nodded agreement -and permission-, jerkily getting up from his crouch and going to wrestle a door open. He'd helped Rodney to it and had given in to the reflex to give the man a quick hug and pat on the back before stuffing him in his hiding spot and closing him in.

Now, staring at a flickering terminal across the room, John tried to decide what to do. Their radios hadn't worked since the alien ship had appeared, so he had no way of knowing if anyone else lived after two hours without Atlantis' help. For all he knew, he and Rodney were the last. If only he'd had time, when this crazy game of hide and seek started, he would have set the self-destruct himself and at least kept the secrets of the Ancients out of enemy hands; but it had all been too fast. Only the fact that he'd felt ridiculously reassured with have a P90 strapped on, as he watched the shield get drained, had led to his being armed at all when the shield had finally fallen.

Now. Now he could sabotage Atlantis; spend his life trying to do enough damage to sink the city. Or he could keep trying to make it to the jumper bay and try to get out; although the way that orbiting ship had laid them low, he didn't hold out much hope for that scenario. If only he knew what these damned strangers wanted, he'd have a goal, something specific to destroy. Walking down the corridor with an ear trained for anyone approaching, he pulled out the memory of Elizabeth, fighting the need to beg forgiveness on his knees for this latest failure. Instead, he tried to imagine what she would order him to do. He couldn't negotiate with people who shot first and shot second. He'd already sent as much of his people to safety as he was going to manage.

She would want Atlantis protected. Saved, by preference... but not if it meant being left to murderers. John nodded unconsciously, deciding that she would hate, but in the end approve of, sabotage. Sink her, John. Let no one have her.

He took the next turn and headed for the armoury, detouring to one of their old power modules and rigging it to self-destruct after disconnecting it from the grid. Coming out of the room carefully, he nonetheless missed the lone alien that came around the corner and shot him with some sort of projectile weapon. John threw himself across the corridor, rolling and coming up with his P90 aimed at the guy's head. Unfortunately, the tuck and roll hadn't been enough and he was hit again before getting the alien.

Catching his breath on a sob, he wrestled his shirt off, adrenaline the only thing keeping him moving. He ripped a strip off to wrap around the hole in his calf and then rolled the rest around his waist, trying to ignore the knowledge that even a glancing blow to the stomach was *not good*. It wasn't as though he'd expected to survive, after all.

He shoved himself up by leaning on the wall and on his gun, just able to put weight on his bad leg; whatever 'bullets' that thing had shot, they were way too close to the size of his own ammo. A crutch was the first order of business. Getting Atlantis destroyed *fast* was the very close second.

He'd been rerouted by enemy patrols and had stopped by a weapons locker when he felt the concussion as the power module blew, sending a dazed mental apology to the now deaf city for the pain he was causing -oops, he was slipping into delirium if he was assigning a computer sensations...

Another half hour of planting C4 and setting another power module to blow and he'd gotten shot again. Just a graze this time, but to the temple. And as he fell backwards to the floor, the P90 firing wildly, the fever that had been slowly blinding him wasn't enough to hide the agony. No amount of adrenaline, even if he'd had any left, could keep the pain of trying to put his weight on a damaged calf muscle from overriding him. The burn of god knows what happening in his stomach. The red haze had finished covering his vision; he couldn't see through it anymore, couldn't move against the rush of pain taking over his nervous system.

All to hell in less than half a day.