Title: Entertaining Strangers
Spoilers: Up to The Defiant One in season one. After that, it's AU
Characters: All, including Ford and Ronon. Sheppard's the main character, though, and McKay probably has the second largest role.
Genre: Angst. Action-adventure. Whump (of Sheppard, mostly). Gen.
Word count: 92,500
Summary: Sheppard disappears on a mission, and is mourned as dead. But then he comes back. Friends become strangers, strangers become enemies, and Atlantis itself could fall, unless a group of people are able to recover what was lost.
The story can be read in a single file on my website, here. Alternatively, you can read it in chapter form here, on fanfiction.net