The people of Atlantis are woken up by a devastating explosion, and they soon realize that not only has their entire food supply been taken out, but the Gate is broken and Rodney is badly injured. A mysterious enemy has infiltrated Atlantis, and it is up to John and his team to stop him before it's too late.

Perhaps carrying an injured and unconscious Teyla into the Monastery had been a bad idea for them both but there was no choice in the matter. Mainly Shep Whump ahead but Teyla whump too. Mainly John and Teyla but whole Team will be there...NOW COMPLETE!

Sequel to 'Blood of the Heir'. Set post season 5. Colonel John Sheppard fights a battle he alone can make, but the Legacy of Janus reaches far beyond him. For now, his blood must also play their part. It is the Destiny of the Chosen.

McKay has the worst luck when it comes to jumpers. This time, he's dragging Lorne along for the ride.

After gating back to Earth, John is arrested, court-martialed and thrown in prison for the death of Colonel Sumner. Rodney, fighting against the unjust punishment, breaks Sheppard free. They return to Pegasus, fugitives of Earth and Atlantis, and try to figure out what their life is now and what they are to each other. A remix of ami ven's 'On The Run' series. Slash.

AU from Enemy At The Gate. Returning to Pegasus was never going to be easy. With the Wraith still a threat in that galaxy, Homeworld Defense in disarray from the battle, and Atlantis in need of major repairs, is leaving even possible? Or is Earth once again it's home? And what of the aliens that call the city home? Will life and love find a way? Merged!

AU. The war continues as a new enemy emerges, the prophesy is far from complete and the stakes are only getting higher. John/Elizabeth, Ronon/Teyla, Carson/Laura.

In an Alternate Reality, Ronon and John return to Earth and run into trouble.

John is heading back to Earth for rehabilitation after the shocking injuries he received in the story "Intensity." He is not happy or impressed when he finds out that he will be staying with his brother Dave. Very soon he is wanted for his unique abilities and he desperately needs help from his friends from Atlantis and the SGC. A sequel to "Intensity".

[ENGLISH] The mysterious recipient of Zelenka's Letter from Pegasus. His fifteen-year-old daughter has been trying to get in touch for almost half a year now. (More slice-of-life than anything. Includes angst, dramatics, humor, romance, and adventure. Very little plot, and very, very long. A relaxing story, I hope.)

"Colonel… We lost Doctor Weir on the replicator planet. Can you lock on her locator beacon and beam her up?" What if Carter managed to get Elizabeth to the Apollo before the replicators made it impossible?

When Ancient tech causes a problem which turns into a disaster for all of Atlantis. who will live and who will perish.

John wants to get back to Pegasus. Too bad everyone seems determined to stop him. Between the IOA, the brass, & general idiocy it looks like Atlantis is stuck on Earth. At least there's stuff going on at the SGC to keep him occupied, right? A conspiracy against the Tau'ri unfurls. Attacks on multiple fronts; kidnapping, invasion, piracy, a bomb. Amidst the chaos, who's the target?

Purple fruit, table dancing Rodney and inebriated John. Elizabeth will certainly have her hands full.

Cpt. Alice Riley is a member of SG4, before she is given the opportunity to join the Atlantis expedition, where she meets Major John Sheppard. This story is an -almost- episode by episode account of Riley's time in Atlantis. The idea is based on if another female member had been apart of Sheppard's team. Sheppard/OC pairing, but it will be a long-burn story, so stick with it.

Is it real or isn't it? Truths must be faced before Atlantis can reach its TRUE potential. This story was written for my friend Callie, who insists that others would like it, too...so here we are. ***REVISED AND UPDATED!***

John Sheppard and Teyla are marooned on a cliff in a planet with extreme weather conditions. Whump ahead. My first fic... NOW COMPLETE!...thanks to Antibodes for lovely review!

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)

Continuation of Midnight Blue. Alice Boyd, now a captain in the U.S. Air Force, joins the Atlantis expedition, something she did not want but felt her duty to accept. Finding herself in the midst of a full-blown war with the Wraith, she will have to overcome her fears, make difficult decisions, and do many things she is not prepared nor trained to do. OC with no AU - post season 5.

"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.

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.