I, Rodney by Alex
Stargate Atlantis | Season 1 AU | Novel, complete

An AU in which Rodney is a robot.

See No Evil by Greyias
Stargate Atlantis | AU | Novel, complete

In a world with no Stargate program, Sheppard gets a civilian job as a test pilot - but secrets surround both the company and new scientist Rodney McKay.

Displacement by smilebackwards
Stargate SG-1/Atlantis | Atlantis Season 3 | Short story, complete

While stuck on Earth, Sheppard finds himself unofficially adopted by the members of SG-1.

-.-. --- -. -. . -.-. - .. --- -. by Mad Maudlin
Stargate Atlantis | Season 4 | Short story, complete

An offworld accident leaves Rodney reliant on Morse Code for communication.

Running On Empty by Sholio
Stargate Atlantis | Season 2 | Novel, complete

McKay and Sheppard are made into Runners by the Wraith, but Sheppard has a little amnesia problem...

Castaways by Baroqy
Stargate Atlantis | Season 2 | Novel, complete

Sheppard and McKay are marooned on a planet with no hope of immediate rescue... and some nasty alien parasites.

The Killing Frost by Sholio
Stargate Atlantis | Season 2 | Long novel, complete

The Daedalus crashes on an icy planet, and somewhere among the survivors is the saboteur...

And All the World Beneath by Jenn
Stargate Atlantis/Supernatural | AU Futurefic | Novel, complete

In a post-apocalyptic world, Dean Winchester meets John Sheppard.

I've Got You Under My Skin by Wraithfodder
Stargate Atlantis | Season 1 | Novel, complete

Sheppard and Zelenka become trapped together on a planet with a nasty secret.

The New Frontier by Sarah T.
Stargate Atlantis | Futurefic | Novelette, complete

After the Wraith are gone, a stranger named John arrives at a family ranch...