Disclaimer: This is a work of fiction. I do not, in any way, own or posses rights to any part of Stargate: Atlantis. I do, however, own the original characters and plotline for this story. These original characters are not based on any other person, either living or dead, and any similarity is entirely coincidental.

Author's Note: This idea came to me while sitting in church, of all places. It's an AU and picks up during "Seige, Parts One, Two, and Three." I am returning to one of my first loves in fanfic: OC development. There's a lot of OCs in this story, and I hope you'll enjoy them as much as I have. I know the characters say John S. and Elizabeth W. This is NOT a Sparky fic. They just happen to be the two central characters of this story. Also, I am issuing a general spoiler alert for at least all of Season One through Three. A really big thank you goes out to theicemenacefor help beta-ing and brainstorming this story. It's a much bigger, much more sweeping plot than I usually write, and that sometimes gets away from me. This will be posting on Monday through Friday, leaving my weekends to work on other ideas. I know most of the first chapter will seem like episode rehash, which most know I usually avoid. I assure you that it was necessary this time. And a warning: minor character death in the first few chapters. While this is a somber opening chapter, I hope you enjoy the story! ~lg

oOo

"May I have your attention, please?" Dr. Elizabeth Weir stood in the control room, the silence around her barely a few moments old. After identifying herself, she continued, "Our plan to stop the Wraith armada has failed. They will make it to Atlantis. Therefore, we must begin our evacuation plans. I wish I could tell you all that this is a fight that we will win, but I can't do that. I wish I could tell you that we will find a safe harbor when we leave here. I can't promise you that, either. I can tell you this: up to now, you all have accomplished extraordinary things, and I believe that even in the face of an uncertain future, as long as we stay together, we have a chance to continue to do so. Now, we all have our evacuation duties, so thank you—and I'll see you on the other side."

The control room fell silent for the space of a moment. In that moment, Elizabeth ran through all the things they had done to fend off the Wraith. Their final attempt, the Ancient weapons platform, had been destroyed, killing Peter Grodin in the process. Now, all they had left was the city's self destruct. That, and a virus created to delete the Ancient database. Elizabeth turned to Zelenka. "Put the virus program on standby."

As of that moment, Atlantis stood ready to die.

oOo

"Colonel Everett!" Elizabeth stood at the base of the stairs to the gate room, holding the piece of paper that officially turned command of Atlantis over to Dillon Everett. "Fine. You're in charge. But I should be at that briefing."

Everett turned to stare at her. "When it comes down to any other aspect of Atlantis, I will be happy to include you. We are talking about our tactical position."

"I understand that. . . ."

"Good." Everett continued up the stairs. "Somebody wanna please turn off that self destruct?"

Elizabeth continued to stare, hating that she'd been summarily dismissed. Never in all her life had she felt so disrespected. Was it because she was a civilian? Or a woman? No matter. If Everett intended to cut her out of Atlantis's defense, he'd be sorely disappointed. Either way, the self destruct needed to be aborted. "Rodney, would you help me, please?"

Moments later, she and McKay entered their access codes that aborted the self destruct. Elizabeth rocked back on her heels, taking a few seconds to enjoy the idea that Atlantis would see another day. The Ancient database could be saved. They could possibly go home, now.

Seeing Sheppard reach for the DHD, Elizabeth held up a hand. "Major, wait."

Sheppard turned. "I have orders to recall those at the Alpha site."

"Not until I've spoken with Everett." She met his eyes. "I'm sure you'll agree that I don't need to be cut out of this. I know as much about Wraith tactics as you do, and I know a lot more about this city than he does. Just give me a few moments."

John stared at her, clearly running through the last few days in his mind. She was right, and he knew it. Finally, he nodded. "Let's go."

Hours later, after learning Everett's plan to defend the city as well as seeing the first wave of Wraith Darts, Wraith beaming into the city, and a host of other problems, Elizabeth walked into her office. She'd just come from the Genii home world after securing use of two of their atomic weapons. The hope that her success stirred made her smile briefly.

That smile faded, however, when she saw Everett in her chair. Try as she might, she couldn't bring herself to like the pompous Marine colonel. It probably had a lot to do with his dismissal of her as the leader of the city. Or it could have just been the man, himself. She'd known plenty of high ranking military men in her time, and Everett was one of the most arrogant she'd ever had the displeasure of knowing. "Colonel."

Everett looked up at her. "Well done, Doctor. I—I have to admit it. I'm impressed."

Elizabeth barely held her smile of triumph at that. "Well, maybe there's hope for me, yet."

oOo

"You let Sheppard fly that Jumper?" McKay asked in shock.

Elizabeth turned away from him. She couldn't answer him. Not with a steady voice. She'd known John Sheppard to be a good man from the moment she first saw him. Now, she knew him to be a selfless man. He'd just sacrificed his life to save the city, and to save Earth. Right now, she couldn't think about her own loss of a friend. This was war, as Zelenka had said. And, in war, there were casualties. Sometimes, those casualties were friends she sent to their deaths.

Finally, Elizabeth turned to Rodney, shaking both of them from their thoughts. "Help me arm the self destruct in case this fails."

As she entered her code, Sheppard's voice came over the radio. "They haven't detected my approach. Weapon is armed and ready. I'm goin' in."

oOo

The Wraith were in Atlantis. Dr. Rodney McKay knew that, but seeing it was completely different from knowing it. Ahead of him and two Marines from Daedalus, two Wraith drones tinkered with a wall. Rodney looked at the Marines with him. "That's the way we have to go."

The lead Marine held up a hand to silence him. McKay actually appreciated the man's patient expression even though he wanted to talk his way through this. Somehow, he found comfort in the sound of his own voice.

After taking positions crouched behind crates stacked as barricades, McKay turned to the lead Marine. The man made complicated motions with his hand, thoroughly confusing McKay. "What was that? I didn't get all that. What do I do? Look, I'm getting good at the rolling things. Maybe I can, uh. . . ."

Again, the Marine motioned for silence. McKay clenched his mouth shut and resolved to wait this out. These men clearly knew what they were doing. They drew both drones away from the path, killing them in turn.

The lead Marine glanced around. "Clear." When McKay stood, he said, "No, you stay here-" His words cut off into a groan as a stunner bolt slammed into him. Seconds later, his companion also went down.

McKay turned to see a third Wraith drone that had appeared from somewhere. With both Marines down, Rodney knew he had to protect that ZPM. Setting aside the case, he straightened. "So, this is how it's gonna be, huh? Just me?" Another Wraith joined the party. "Okay! That's just fine!" He yanked his pistol from the holster. "You want some of this? Huh? Huh?"

McKay tried to squeeze the trigger like he'd been taught, but his thumb touched the wrong part of the gun. Rather than firing, he ejected the clip. As it clattered to the floor, he struggled to breathe. "This is McKay—I'm in trouble down here!" A stunner bolt cut off what else he was about to say.

Some time later, he opened bleary eyes to see a form over him. "Teyla?"

"Rest, Rodney. I am here with you."

"We thought you were. . . ."

"My radio was broken, and I was separated from my group." Teyla glanced around. "I have been trying to make my way back."

For a moment, McKay let himself relax. Then, he remembered the crate that Daedalus had beamed into the control room. He pushed himself up. "The ZedPM. Do you see it? It's in a crate. . . ." He looked around quickly, seeing nothing that resembled the crate he'd been carrying. "Oh, God! It's gone!"

oOo

"Elizabeth, you've got a problem!" Major John Sheppard stared out the viewport of the Daedalus as Wraith Darts headed for the city.

"Yeah, we see that, Major." Elizabeth's response was terse, as if she was waiting for something.

"We're moving to intercept, but I don't think we can get there in time."

"Not a chance," said an unfamiliar voice over the radio. "They're coming in too fast."

"Oh my God!" Zelenka's panicked voice filled the bridge of the Daedalus. "Their approach is ballistic."

"What does that mean?" Elizabeth asked.

John shook his head. "They're going Kamikaze. You'd better get that shield up!"

"We can't." McKay's voice sounded defeated. "The Wraith have the ZedPM. I could do nothing to stop them."

The news rumbled through the bridge of the Daedalus like a boulder rolled through the center of a village. Sheppard braced himself on a bulkhead and tried to breathe. "They what?"

"I'm sorry!" McKay yelled. "But what was I supposed to do? I was unconscious!"

"Okay, now is not the time to argue!" Elizabeth also sounded put out, but she forced a calm tone into her voice. "Rodney, you did all you could do."

Seconds later, the Darts impacted Atlantis.

oOo

Hours later, Sheppard stood on the bridge of the Daedalus, staring as twelve Hive ships dropped out of hyperspace. A blue and green planet whirled below them, but no one lived there any longer. The planet had a Stargate, and Sheppard wondered if the Wraith intended to try to gate into Atlantis.

Thinking about Atlantis made him wonder how the evacuation was going. Somehow, the main tower of Atlantis had survived the Wraith Kamikaze runs, and he'd beamed in with Marines and a few Air Force personnel to help with evacuation. Atlantis was in pieces. Elizabeth had ordered everyone except the most crucial personnel through the gate to the Alpha site. When they discovered the twelve Hives heading their way, Sheppard joined Caldwell on the Daedalus, leaving a new arrival, Major Lorne, in charge of helping Elizabeth evacuate the city.

Over the comms in the ship, Novak spoke. "First weapon away."

Outside, one Hive exploded. Behind Sheppard, the weapons officer said, "That's a kill."

"Stand by," Novak said.

A second Hive exploded. Sheppard nodded. "Alright. It's working."

The weapons officer studied his screens. "The other Hives are altering course to intercept."

The next several minutes grew tense as the Wraith blocked the transport of any other nukes aboard their ships. They also flanked the Daedalus, intent on boarding the Earth ship. Sheppard braced himself as the ship rocked from numerous hits.

"Rear shield emitters down to forty percent!" The weapons officer scowled. "Ventral rail gun two is out of action!"

"Main engines to max." Caldwell's voice betrayed his tension. "Try keeping the damaged shield from their main force."

"Sir!" The weapons officer drew their attention again. "One of the cruisers is approaching on a parallel course."

"They may intend to board us." Sheppard stood next to Caldwell's chair. "That was their strategy when they attacked Atlantis."

Caldwell looked to his right. "Shield status?"

"Under twenty percent."

"Set course for Atlantis." Caldwell turned to the viewport. "Engage hyperdrive."

At that moment, the ship rocked forward, and alarms blared through the bridge. The weapon's officer blinked. "Rear shields are down!"

Another blast rocked the ship. The helm, to Caldwell's left, stared at her screen. "Hyperdrive is down! That last blast took it out!"

Caldwell glared at the viewport for only a moment. Then, he hit the button on the arm of his chair to activate the shipwide comm system. "Attention all hands, abandon ship. Get to your beam-out points. This is not a drill."

Sheppard saw the effect that announcement had on Caldwell. This ship was brand new. It had Asgaard technology, along with every advancement Earth had to offer. And, yet, they had lost. Sheppard hauled the weapons officer from his chair and pushed him toward the front of the bridge. He would have taken the seat, but Caldwell stopped him. "Get out, Sheppard. Atlantis will need you to tell them what happened here."

Sheppard wanted to argue. But he knew the truth to Caldwell's words. He nodded. "See you on the planet's surface, Sir."

As the light of the Asgaard beam engulfed him, John Sheppard knew he'd seen Colonel Steven Caldwell for the last time.

oOo

Elizabeth stood in the control room of Atlantis, watching the final few souls make it through the Stargate. The city was in shambles, the systems barely functioning enough to sustain a stable wormhole. Major Lorne, the officer Sheppard left in charge of the evacuation, pushed Zelenka and Carson through ahead of him, giving Elizabeth a nod. They'd saved everyone they could save. There was nothing left to do besides enter her code. By doing so, she'd initialize the self destruct and release Zelenka's computer virus into the Ancient database.

As she typed her code into the computer terminal, the wormhole destabilized and shut down. Elizabeth knew a moment of panic as she realized she might die here. After entering her code, she rushed to the DHD and began dialing. Power reached the gate because it activated. In her haste, her hand slipped on the crystals, but she didn't notice. The city could blow at any moment. As the wormhole vortex kawooshed into the room, she grabbed the final laptop containing a miniscule amount of the Ancient database and rushed forward. An explosion sounded in the distance, and the blast wave carried her toward the active gate. She flew through the wormhole. Shrapnel and flames followed her as she somersaulted down stone steps and into the sand. Her laptop, useless now, lay in pieces around her. Elizabeth held on to her consciousness long enough to see the gate shut down.

Atlantis was dead.

"If your descent is from heroic sires, show in your life a remnant of their fires."
Nicholas Boileau, French poet and literary critic
1693-1711

~To Be Continued~