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..

"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.

John and Teyla are back in their own time after their adventure in the future. Rodney is determined to find Arastica in the past as is John. John has the coordinates for Sheppard's planet and Woolsey's given him the go-ahead to find it. Wraith, visitors from the future and time travel all add up to a bad week for John and the team. A sequel to 'A glitch in time.

Takes place after Critical Mass (Episode: 2.13) How would Caldwell have been if he'd had a daughter and she'd figured out the code?

She was an ice queen. He was the unflappable Major. She caught his eye but could he melt her frosty exterior.

Atlantis had been on Earth for 3 years, when a new computer program activated and lead them to The Depot. Will this is a wonderful treasure, or will it expose the stargate for all to see?

Sequel to my other Story Murus sees John Sheppard once again reunited with Bee. Teyla, Rodney, Ronon and Carson make six...and off we go... Drama, H/C, angst and friendships are a given. NOW COMPLETE!

A feeling of absolute terror overcame him as he approached the person and much to his horror, it was indeed his evil twin and the look on his face was one of pure hatred. "Do you think that you could get rid of me that easily? "The entity snarled. This had to be a dream, the entity was dead – wasn't it? What if the Evil Sheppard didn't leave him at the end of Doppelganger?

When giant salamanders take over Atlantis while Sheppard's team is off-world, it falls to Doctor Zelenka to save the day. Except he's not sure he's cut out for this kind of heroism.

Queen Raynelle Dawn, last of her kind is saved from the Wraith by the Stargate Atlantis team. They quickly come to realize that she may be their greatest weapon against the vampiric species. Both Ronon and Sheppard harbor feelings for the new arrival, but which one will she choose? How will her presence impact Atlantis?

When the opportunity arises to trade for a ZPM, Colonel Sheppard is faced with a tough decision. Is he really prepared to do what is asked of him? But how can he refuse, when the fate of the expedition might depend on him? Sheppard's gene gets him into trouble, but not just in the usual way.

A little story, built around an oil pastel painting (find it on AO3 or Tumblr). Rodney and John are (reluctantly) are on a quest...

Stargate The Twins is a sequel to Stargate Atlantis / Universe. It is a comedy, and a bit of a spoof of both TV series.

What if not all of the Ancients left Atlantis? What if they left defenders behind just in case? Canon compliment for season one. starts just after the ZPM arrives from the Daedalus

How hard can it be to make sure an Ancient device stays off? Sheppard and the Atlantis expedition's Chaplain (OC) go offworld and get into a spot of bother. Set in season 1. Gen. Warnings for violence, trauma & some bad language, and a tiny bit of religion. Rating: M to be on the safe side. Reviews are welcome. I'll aim to finish this by Easter, hopefully!

After his rescue from the sunken jumper, the last thing Rodney wants is to be around more water. Unfortunately, the team's next mission is to a planet made up of island city-states where Sheppard and McKay become unwitting pawns in a trade war. (Part 12 of Team Rebuilding) Post s2e14 Grace Under Pressure

Captured with some new Allies, and forced to work in dangerous mines are Sheppard, Ronon and Rodney's new fate. Sheppard, harbouring a secret, is also forced to activate several artefacts under duress, whilst his friends' and two persons of interest watch over him.- one with increasing fascination and one in silence.

Teyla looked at the tall messy-haired man in front of her and she had no idea who he was. Had she met him before? She had no idea. Teyla angst and Shepwhump in this tag to season three's episode 'The ark'.