95Lt Colonel John Doe » by Sarahzilla Col Sheppard has amnesia and Atlantis doesn't know where he is, and when Rodney returns without his memory too, foul play is suspected.
Stargate: Atlantis, T, English, Adventure & Mystery, chapters: 18, words: 34k+, favs: 12, follows: 42, updated: 1/7/2012 published: 2/24/2006, John S., Rodney M.
327Guarding the Shepard » by Kidwrangler Sheppard investigates a series of seemingly unrelated accidents in Atlantis.
Stargate: Atlantis, T, English, Adventure & Humor, chapters: 15, words: 46k+, favs: 144, follows: 200, updated: 7/28/2009 published: 2/16/2006
417 Alisa » by Una Spectre AU There's more than one McKay on Atlantis.
Stargate: Atlantis, K+, English, Family & Drama, chapters: 55, words: 141k+, favs: 116, follows: 85, updated: 5/11/2009 published: 4/10/2006, Rodney M.
41Backyard Menace » by Mazeykins Takes place shortly after Lifeline and landing on their new planet M35-117. Sometimes accidents happen in your own backyard. Team fic and Rodney whump.
Stargate: Atlantis, K+, English, Drama & Hurt/Comfort, chapters: 10, words: 13k+, favs: 26, follows: 49, updated: 11/29/2008 published: 1/15/2008, Rodney M., John S.
182Mutiny in the Infirmary » by Wolf Maid Sheppard wants out of the infirmary, but how he got in there in the first place could cause trouble of a loss-of-inhibitions-"Virus?" kind. Mostly humor, with large doses of insanity. Shweir, FordTeyla, McKaySora
Stargate: Atlantis, T, English, Humor & Adventure, chapters: 22, words: 17k+, favs: 41, follows: 72, updated: 9/6/2008 published: 10/1/2004, John S., Rodney M.
25And then the bad guys were high » by Belisse Atlantis is caught with its pants down… to the ankles. Last in the Friends are Foes Series, with that comes romance many pairings but the main one is SW, humor, violence, group whump and an evil bad guy.
Stargate: Atlantis, T, English, Humor & Adventure, chapters: 9, words: 20k+, favs: 5, follows: 10, updated: 8/2/2008 published: 3/23/2006
2k+Memoranda From the Edge » by Dr. Dredd Elizabeth has decided to create a bulletin board for the posting of important notices. This series of ficlets, drabbles, and other madness is the result. Spoilers for Return, Parts 1 and 2.
Stargate: Atlantis, K+, English, Humor, chapters: 166, words: 56k+, favs: 429, follows: 267, updated: 6/24/2008 published: 7/31/2005, John S., Rodney M.
551 Breaking Walls » by TechnoScribe Circumstances, and Rodney's friends, won't allow him to keep his past a secret anymore. A veritable McKay Whumpathon! Warning! Spoilers. Lots and lots of Spoilers. Ever so slightly AU. Final chapter posted.
Stargate: Atlantis, T, English, Suspense & Friendship, chapters: 31, words: 140k+, favs: 436, follows: 206, updated: 4/17/2008 published: 4/17/2006, Rodney M.
552 The Hitchhiker's Guide to the Pegasus Galaxy » by Seanait John decides to put down a few guidelines.
Stargate: Atlantis, K, English, chapters: 25, words: 30k+, favs: 75, follows: 75, updated: 2/14/2008 published: 12/24/2005
815 Going Home » by Titan5 John is sent back to Earth to recover from his latest set of injuries and decides to visit his father. He is very surprised at the homecoming he receives.
Stargate: Atlantis, T, English, Hurt/Comfort & Angst, chapters: 20, words: 95k+, favs: 404, follows: 169, updated: 11/24/2007 published: 10/8/2007
122The Artifact » by Ognonamis After the team comes in contact with a small artifact, odd things begin to happen to Colonel Sheppard. Chapter 17 is up FINALLY! Please, read and review.
Stargate: Atlantis, T, English, Drama & Romance, chapters: 17, words: 34k+, favs: 18, follows: 36, updated: 10/13/2007 published: 6/5/2006, John S., Teyla E.
307 Unexpected » by oparu-inactive Response to a challenge on Command Dynamics. Just before the Lanteans send them home, Sheppard and Weir wake up together on an alien planet. The war with the Replicators begins after they retake the city and find out Elizabeth is pregnant.
Stargate: Atlantis, M, English, Romance & Drama, chapters: 32, words: 222k+, favs: 134, follows: 99, updated: 9/6/2007 published: 10/6/2006, Elizabeth W., John S.
46 Belonging » by Ammanalien Lorne observes Sheppard's team, and wonders where he fits. Then events take a serious turn... A little story where Lorne gets whumped.
Stargate: Atlantis, T, English, Hurt/Comfort & Angst, chapters: 6, words: 9k+, favs: 77, follows: 16, updated: 8/15/2007 published: 6/30/2007, E. Lorne
213 Shattered » by SGAFan A close shave with death leaves John Sheppard searching for answers. Warning: Shep Whump!
Stargate: Atlantis, K+, English, Drama, chapters: 11, words: 38k+, favs: 81, follows: 63, updated: 8/5/2007 published: 2/22/2007, John S.
203Under the Mud » by Splitbeak A visit to a village covered in mud leads to a captured Colonel, and an unexpected alliance with an old enemy. Shep whump. Dark fic.
Stargate: Atlantis, M, English, Angst & Adventure, chapters: 23, words: 71k+, favs: 35, follows: 89, updated: 4/30/2007 published: 5/16/2006, John S., Rodney M.
334 Mind Over Matter » by Dr. Dredd John starts to exhibit telekinetic abilities after returning through the time dilation portal. Takes place between Epiphany and Critical Mass, spoilers for Epiphany and Condemned. COMPLETE!
Stargate: Atlantis, T, English, chapters: 17, words: 38k+, favs: 180, follows: 109, updated: 4/24/2007 published: 1/27/2006, John S., Carson B.
317 Whirlwind » by NotTasha The team is helping out a town with a broken shield system, a penchant for tornados and a secret. McKay has a building fall on him. He gets hurt. Sheppard, Teyla, Ronon and Beckett along for the ride
Stargate: Atlantis, T, English, Adventure & Hurt/Comfort, chapters: 17, words: 53k+, favs: 152, follows: 41, updated: 4/21/2007 published: 4/3/2007, Rodney M., John S., Carson B., Ronon D.
518 Never Stop Moving » by Tipper Chases, explosions, head wounds, twisted ankles, damaged ships and a desert serve as the backdrop to a rescue mission that doesn't quite go as planned. In other words, a typical Atlantis mission o' mayhem. Team Fic.
Stargate: Atlantis, T, English, Adventure & Angst, chapters: 23, words: 88k+, favs: 109, follows: 43, updated: 4/21/2007 published: 3/17/2007, Teyla E.
62 Deadly Assumptions » by blueoctober A simple mission to a new planet...no problems right? A team story with Carson.
Stargate: Atlantis, T, English, chapters: 14, words: 37k+, favs: 5, follows: 17, updated: 4/15/2007 published: 6/3/2006
806 Maybe I'm Dead, I Just Haven't Stopped Moving Yet » by cybersyd42 The consequences of a mission gone wrong have a devastating impact on the SGA team. COMPLETE!
Stargate: Atlantis, K+, English, Angst & Drama, chapters: 29, words: 119k+, favs: 209, follows: 115, updated: 3/4/2007 published: 9/10/2006, Rodney M., John S.