The Guardian was left behind to protect the city until her people returned. After waiting for millennia she finally despaired, only to be re-awakened unexpectedly by strange humans from Earth who had shockingly interbred with her own race. Upset and confused, she takes control of the city from the humans as she plans her revenge against the Wraith. AU starting at ep 4.

Well... I was just informed that I had died. Then I was told that I have been chosen to be reborn. A floating panel with questions on who I want to be and where I want to be reborn pops into existence. And so, I chose the Stargate franchise. Lets hope that I chose wisely.

This is the tale of Ila Ultum, a Lantean that got sent 10,000 years into the future, escaping from the Wraith that were at war with the Lanteans. Join him on his journey where he meets the Atlantis Expedition, takes the fight to the Wraith and keeps the legacy of his people alive!

When an off-world mission goes sideways, Rodney is forced into a position that may destroy the trust he's been rebuilding with Sheppard, and John finally accepts that 'no one left behind rule' he put in place is there as much for him as it is for his team. Post episode s02e08 Conversion. (Part 7 of Team Rebuilding series)

For ten millennia, the Ancient city of Arcadia has slumbered. As the United Kingdom steps into the intergalactic stage on its own, they come to discover a once great power in the Pegasus Galaxy. Settling in is just one part of the adventure, however. Politics, enemies and discoveries await the Pegasus branch of the United Kingdom Expeditionary Service. Rated M for future themes.

A series of missing scenes and vignettes for Stargate: Atlantis. Canon compliant, although with rather clear hints of John/Elizabeth.

'The course of true love never did run smooth,' and especially not if there's a Wraith in your midst. Doubt and suspicion lead to misunderstandings and mayhem in this romantic drama in five acts! Rodney/Jennifer, Ronon/Amelia, Teyla/Kanaan, John/Teyla

John is exploring Atlantis when he accidentally ingests some hallucinogenic algae. Terrified and alone, he has to rely on Rodney to rescue him and bring him to safety.

The team struggles to get back to Atlantis with a desperately-injured John after Ronon participates in a Gladiator-style fight that goes wrong.

John's thoughts during The Eye, one shot with hints of John/Elizabeth

Years after the team returned to the pegasus galaxy the team goes to a planet mysteriously unharmed by the wraith. They are suspicious until they arrive and find out why. (Btw I happen to really like Carson and Elizabeth so I'm keeping them ) This is my first story so I am still new to this please review with any suggestions I will try to update every other day! Also more characters

While a new enemy approaches, there's an old one running rampant throughout the galaxy. Mia's got a lot cut out for her this time around, but at least she has John and her friends by her side. And those who play with fire always get burned. John/OC Book 3

John and Rodney meet long before the Atlantis expedition and spend many years worrying that the other will (metaphorically) kill him when they've each screwed up, respectively. McShep, pre-canon to post-canon.

Four children make friends and explore. [My take on the classic de-aging trope!]

Coming to her office and 'disturbing' her to make sure she took a break or ate something had always been his habit and became a norm after they got together. He knew exactly what she was like when she was focused on her work and it wasn't this.

The heat and dust of a desert world lead to frayed tempers and irritation. And then things get worse. Come on team, you love each other really!

After a long day of trade negotiations, the team is offered accommodation for the night. It's not long before an argument is brewing between Rodney and the rest of the team. John decides that he'd rather take his chances outside in the storm than have to listen to Rodney. Very soon John runs into some wild beasts and he will definitely need help from his Atlantis family.

PART 6 of the 'NEXUS' series. After the harrowing events of 'The Attack', Woolsey, Chuck, Nexus and Juno are in recovery. The return of the Commander (Todd) heightens the conflict until he provides a gift that turns things around… Disclaimer: Stargate Atlantis is the property of MGM. Only Nexus and Juno are mine.

The real Sheppard had come into his dream and tried to protect him and goddamn if Rodney's subconscious couldn't stop fucking reading into that. So maybe it hadn't been the whale nightmare again, but he never fucking asked for this. (McShep pre-slash)

Gulping, John closed his eyes and focused on his breathing. One, two, steady. In and out. Hold it. One, two. It took a couple minutes before he could slow his heart rate back down and feel…normal again. Well, as normal as he could feel, given the circumstances. He wondered if anyone else was still feeling aftershocks like this. (includes McShep pre-slash)

When Ronon, John, and Rodney are exploring an Ancient Lab, Ronon accidentally inhales a substance that causes him to think John is his enemy. Rodney and a badly-injured John must find Ronon before it's too late.

After The Lost Tribe, AU. Now that Jennifer has made the choice, she becomes more overt in her affection for Rodney. After spending a pleasant evening amongst friends, Jennifer bets Rodney that if he had a girl in his bed, he'd be unable to resist temptation. Rodney swears that he would have the utmost discretion. Rated M for later chapters.

It was all he had left. The pot and the stupid mark on his wrist, which simply refused to disappear, mocking him with its unchanged state. Soulmate AU (but sticking mostly to canon)

John has to participate in a ceremonial drinking contest in order to secure a trade deal for Atlantis. The only problem? John can't hold his liquor.

A team disappears while on a mission to a sinister underground city and John and his team are sent to investigate. How will they uncover the truth, amidst the shadows and deceit?