With the growing threat the Wraith could attack Atlantis at any moment, Sheppard's team travels to Haven, one of the planets on Alt!Elizabeth's list, looking for a second ZPM to power the city's defences. During their search, the team discovers that Haven is hiding a few surprises, and Ronon is faced with a life-changing decision. Post s02e18 Michael Part 13 of Team Rebuilding

"Vegas" Universe: Police Detective John Sheppard joins the Atlantis team, but thinks it's not him they really want, it's the other John, the hero John, Ronon's BFF, McKay's idol. Figures that, the sooner they realize he's not him, the better off they'll all be. No Slash.

Sad McKay oneshot just read it it's less than 1k you don't even have to review if you don't want

He had no idea who he was or how he'd ended up on the chunk of rock he was on. But in the back of his mind, he knew that someone was missing him and they would be searching for him. With the help of his new friend, he knew that he must somehow survive until help arrived. An AU for season five's 'inquisition.'

It started with a big, bright light and then Atlantis, on it's way back to Pegasus from Earth, finds itself in a unknown galaxy. Tragedy strikes early on - will they stay together safely and make their way back to Pegasus?...read on and see...and yes, whump for a certain Colonel is a given! Torren makes a big appearance in this story. I will look after him, I promise!

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Ronon and Sheppard are trapped, injured, and alone on a distant planet. Hunted by people who possess a sadistic weapon, Ronon has to keep Sheppard alive and hope for rescue which may not come in time.

A young wraith finds herself in the hands of the Lanteans. What do they want with her? What does she want? A story of healing and self-acceptance. Warning: later chapters will explore depression and suicide

Colonel Carter, back in command of Atlantis, has discovered the Ancients’ lab for making ZPMs. Atlantis is once again back at full power and goes on the front line. Her first mission is find Destiny and bring her to better than new condition. As more ZPMs get finished, this power will change the tide in 2 wars. The Earth fleet sees its numbers swell, her ships equally well powered.

When mysterious aliens kidnap Sheppard and use him to try and take over Atlantis, it's up to the team to save him. Inspired by "The Daedalus Variations," this is the AU take on what the team was doing fighting the aliens on one of the Daedalus ships in the alternate timeline. Lots of Shep whump and team angst to follow ...

"La rumeur est la fumée du bruit." Petit OS Shweir un peu guimauve mais pas trop.

The team is trapped in another, frightening, reality.

Evan wants to transfer to Atlantis. Caldwell wants to make sure that Evan knows that he will always have a home.

A distress beacon rang out on the planet, they went to investigate, thinking they would find nothing. What they, no who they found, were long presumed dead. Now they stand before them craving to the place they once called home...

After a run in with a unique device, Sheppard, McKay, Ronon and Zelenka end up on a body swapping nightmare.

Atlantis is back in the Pegasus galaxy and everything is changing. John decides that he can't deal with it, so he decides to go and spend a few days with Carson, who has recently left Atlantis to treat the sick and injured off-world. With too much to drink and a black spider, things don't go well for John and he ends up back on Atlantis in the infirmary.

Sheppard and his team (sans Teyla) are offworld and run across some hidden ancient ruins. The next moment, they are in Tampa. Sheppard was hungry, what can you say...

The Atlantis Expedition have Captured some Replicator warships and are using them to shape the future of the Pegasus galaxy and their War against the Wraith. See how the Atlantis Expedition Begins to use their own Human-Replicators to help in their war against the Wraith and discovering New/Old Ancient warship designs of ships to fight the wraith.

Sheppard's team is headed back to Atlantis when everything goes terribly wrong. Stranded deep in an unfriendly forest, danger is closing in and they must rely on each other to survive until rescue comes. Set in mid Season 3. New Chapter 35 created to tie up a loose end.

Todd comes to Atlantis to discuss alliance, but Sheppard is off world on a mission. Major Lorne is left keeping him company, in addition to his regular XO duties. Things dont go as planned. Todd/Lorne, after series finale but before Legacy. Rated M for language, eventual light smut, slow burn fluff

When Ronon Dex is freed from being a Runner and brought back to Atlantis, he is confronted with culture shock unlike anything he ever expected. Grace Becque is an anthropologist with the expedition who is content to remain in the background. When the two are sent on a mission together, Ronon is tasked with keeping Grace safe in a tricky situation with unexpected outcomes.

Episode I: Nine months after their return to Pegasus, Atlantis is desperate. Increased wraith attacks and IOA scheming have left the city barely stable. But when the aid General O'Neil sends them turns out to be a woman from Sheppard's past, her arrival has resounding consequences that may prove invaluable or, they might just make everything worse...

Daniel is confronting the Vanir leader when the armoured alien reveals a startling secret.

She wasn't meant to be alive. He was never meant to know. A secret, is was she was, born from a human woman, to a species that dominated her galaxy. Hidden away until those people disturbed them. Woke them and now she was in fear of discovery. Her mother was gone, and she was growing sick, but Atlantis might help or kill her. Her "father's" people might kill her too.

Soulmates exist! When it's discovered that John Sheppard has the Ancient gene his twin's DNA is tested and found to carry the Ancient gene as well. Doctor Weir immediately asks John to have his twin fly back home to see if he would be willing to go on the Expadition as well. Randy, to Doc Weir's surprise is John's twin sister who is one of the few people born with two soulmates..