Authors Note: This story is AU, meaning Alternate Universe. Some things will not be canon to the Stargate Franchise, fair warning.
Disclaimer: If you know it, I don't own it. If you don't know it, I still don't own it. The only thing I own is my own warped mind that created this.
John Sheppard groaned as he pulled himself out of the stasis pod. 'This is weird,' he thought. 'I don't remember going into stasis.' Looking down he saw that he was – thankfully – dressed in his usual Atlantis uniform. He looked around the room. All the other pods were devoid of occupants. "Shit. Todd's not here." He muttered. "I sure hope I don't run into him."
John gradually made his way down the halls of Atlantis, his speed increasing the closer he got to the control room. Dust covered consoles greeted him when he finally entered the control room. Light slowly filtered through grungy stain-glass windows. There were no human laptops on top of Alteran crystal consoles. No dust sheets covering said consoles. It was like the Atlantis Expedition had never occurred; no Elizabeth Weir to travel back to watch over the city as it slept. A small tear started to streak down the side of John's face. The single drop tracing a path from his eye to the tip of his nose, where it slowly gathered before falling onto the consol he was leaning over. A small shift of light caught his attention. Slowly he straightened, and made his way over to the balcony door. He had to force the door open, but when he managed to get it open, his breath was taken away.
Atlantis was half submerged in San Francisco Bay. The towers on the piers poked out of the water here and there. Looking up, his breath was stolen once again. Smoke was rising from many locations across the San Francisco skyline. Half crumbled buildings filled the view, many of had burn marks like they were hit by weapons fire. Only the middle of the Golden Gate Bridge was still standing, melted cars scattered like toy cars on the roadway.
A screaming whine filled the air as a flight of Wraith darts over-flew the city; following them was another flight of vessels. John remembered them from a briefing that happened years ago. The second group of vessels belonged to the Ori. Somehow, for some reason; the Wraith and Ori had joined forces to conquer Earth. Another flight of darts screamed overhead, only this time a culling beam hit the tower. The beam washed over John, sucking him into the darts containment bay.
Sheppard groaned for the second time in less than thirty minutes. Culling beams always left him with a massive headache. Opening his eyes, he could barely make out two vague figures in front of him. Blinking a few times, one of the blurred figures resolved into the Wraith that John called Todd.
"I see your awake, John Sheppard. Pity our reunion is in such a manner." Todd said with his usual tone.
"Yeah… give me a sec." John replied. He shook his head, which considering how his head felt, was the wrong thing to do. His migraine increased ten-fold. "Got any aspirin?" he asked, even though he knew the answer.
The other figure made his way towards John. The disfigured face revealed him to be a Prior of the Ori, but the face beneath the disfigurement was that of Dr. Daniel Jackson.
"Light or Darkness; Life or Death; Joy or Despair; those are the only choices that you have. Embrace the Light of Origin or face eternal damnation." The man that was once Daniel intoned.
"Hey Daniel, like the new look. But that might be a problem for me, being an atheist and all…" John shrugged his shoulders.
Prior Daniel sighed, "Another one that rejects the Bliss that is Origin." He took a step back as Todd started forwards.
"I've been waiting a long time to finish what I started on that Genii planet long ago. Thank you for declining the offer, John Sheppard." Todd said as his left hand slammed into John's chest. "Scream, John Sheppard. I know the pain of losing your life essence is painful." Unable to bear the pain much longer, his victim let out a cry, long and loud. Prior Daniel's staff glowed as Sheppard died, funneling his soul to be consumed by the Ori for eternity.
(AN: I wanted to end here but… eh)
"AAAAAAAAAAAAAAAaaaaaaahhhhhh h…." John shot upright in his bed, sweat streaming down his body. Breathing heavily, he tried to settle his racing heart. It was just a dream. 'That is IT!' he thought. 'No more junk-food before bed.'
He swung out of bed, placing his feet on the floor of his room. The cold floor was shock to his system. 'Geez, that's cold.' He tried again. This time the city had adjusted the temperature of the floor so that rather being cold, it was nice and warm. John made his way to the shower, where the city (thank god for his ATA gene) kept the temperature at a constant level. Exiting the shower, John quickly got dressed and made his way to the control tower.
It was the final week. Atlantis was scheduled to depart in less than five days. A new BC-304 was to be assigned to join Atlantis in Pegasus. The Siranui or 'Unknown Fires' was Japan's first inter-galactic space vessel. Her commander, a Colonel Yamato Shiji (Shiji Yamato to Americans), understood that his mission was to protect Atlantis from attack, either internal or external.
The Hammond was severely damaged in the battle with the Wraith Super Hive that attacked Earth months ago. She was damaged to the point that it would be cheaper to use her as parts, rather than rebuild her. Her commander, Colonel Samantha 'Sam' Carter, was asked to be the Atlantis leader once again. Richard Woolsey had stepped down when his sister became extremely ill. He had decided that it was better for him and his extended family if he was close by.
The Apollo and Sun Tzu were also badly damaged but not to the extent that the Hammond was. It was determined that it would be at least six to twelve months till either one was ready for deployment.
Only the Daedalus and Odyssey were in less-than-perfect shape, but they had to stay behind to defend Earth against un-foreseen events.
Atlantis had engaged its surface thrusters the week before, which had moved it out of San Francisco Bay and out into the middle of the Pacific Ocean. Two days ago, Atlantis glided past Hawaii, and met up with the Siranui, half-way between Japan and Hawaii. It was here, in a location where there were no shipping lanes that Atlantis was to depart for Pegasus. Last minute checks commenced as Siranui gently landed on one of the piers. The weapon stocks were full and power was well in the green.
John's headset crackled, Sam's voice, warm. "Ready, Sheppard?"
"Ready as I'll ever be." John leaned back in the chair and closed his eyes, feeling around him the familiar thrum of power.
Visualize the city, resting on the waves. That was easy. He had looked outside one last time before he came down, a golden sunrise, just a bit past dawn. A perfect day, a beautiful day.
The Earth turned beneath them, Singapore wrapped in night, glittering with a thousand lights. The moon set, just as the sun, a bright disk, almost completely above the horizon. Invisible lines of force surrounded them, charted out in lines of blue fire. Were they made by the city or by him? John couldn't tell. Was it that he saw it and the city read it, or that the city spoke to him?
This place, a whisper. This moment. This precise second, this tiny coordinate in space. It filled him, encompassed him, as though he stood on the fulcrum of the universe. He was the city and the city was him. Ready to lift. Engines fired beneath the surface, water rushing away from ducts and vents, simple as moving his hand. The shield rose, trapping air inside the city, so that the occupants could breathe during the trip. For a moment, the City of the Ancients stood like a mirage, surrounded by vaporized water and air.
There were voices far away, Sam and Zelenka, Rodney saying something. They didn't matter. Engines online, inertial dampeners engaged and the city began to lift, like spreading his own wings. It was easy, easy as those dreams of flight everyone has as a teenager, when suddenly you can soar effortlessly as a young swallow. Above, the stars were not a field, but an ocean of infinite depth, millions of bright suns each moving in their extraordinary dance, every point relative.
"Wormhole drive online." John heard Rodney say, distantly. "Ready to jump." Power raced into the drive, power channeled from the three ZPMs. The thrum extended throughout Johns entire body. It was at that point that everything changed. Detected by the city, but ignored by Rodney (who dismissed it as unimportant), a massive solar flare raced towards Earth. The wave pulsed through the city, the shield protecting the people from all forms of exotic particles, save for one. Call it timing, destiny or just an ascended being with nothing better to do; yeah, defiantly the third one. This specific kind of particle, making up only one billionth of a percent of the entire flare, directly affected the crystals in the wormhole drive, changing their internal structure. Atlantis disappeared in all flash of blue light.
Author's Note:
At last my Code Geass x Stargate X-over is up. A bit of news regarding this story; I have plans to take it farther than just Code Geass. You will just have to stay tuned to find out. I never realized exactly how bad my free hand writing is...