Spoilers for S3 The Return. When systems all over the city begin shutting down for no apparent reason, John and Rodney are cut off from the rest of the city. Then Sheppard suddenly collapses, and it's up to McKay to save him, and Atlantis. ShepLantis

On the run with a sick Sheppard, Rodney tries to keep them both alive after being imprisoned. Whump and lots of comfort. Gen.

An accident teaches Ronon more than one valuable lesson. Ronon and SheppardFriendship

There are many dangers in the Pegasus Galaxy that have nothing to do with hostile aliens. After an accident, John finds out the hard way and the Team tries to help him in the aftermath.

Nothing is ever black and white in the Pegasus galaxy. Rodney and John face a deadly threat where time is not the only enemy. Whumping and Angst.

The team are captured and learn that there are two forms of torture, not knowing which one is worse. Lots of Team emotional whump—Shep whump.

Another ancient device cause trouble for Sheppard. You can't get too much John whumping! Rated for the occassional swear word.

[Complete] On a world of masks and lies, the lone survivor of a disaster seeks revenge on his enemies. Contains Shep whump.

COMPLETE: Injured and on the run, Sheppard and McKay are trapped in a dark ruin with a monster. This, however, is soon the least of their problems.

This is for ROO who wanted Shep going crazy with bonus points for whump.

John Sheppard returns to Atlantis alone and struggles with the fact that he left his team behind. Mostly Shep whumping, some team whumping. Friendship only, no slash

John Sheppard becomes the unfortunate target of a group of local drunks.

When things in the Atlantis base become a little too quiet, Sheppard is sent into the deepest corners of his own mind after an experiment backfires. Shep whump and Rodney heroism.

The sequel, or continuation, of The White Room in which John and Rodney get into all kinds of trouble working as slaves and battling Kolya.

Elizabeth goes missing and John is now in charge of Atlantis until they get her back. It's not going well.

Sheppard seems to have lost his mind and no one can figure out why.

When Sheppard and his team go offworld, things don’t go to plan and Sheppard gets beaten, tied to tree and nearly killed by his teammates.

COMPLETE: The gang gate to a world with a deadly secret—will Sheppard and Beckett become victims of genetic exploitation? Sheppard and Carson whump.

Sometimes all that matters are the codes and values you uphold. A deadly vendetta will test loyalties, limits and friendships, with more at stake than anyone realizes. Contains Shep Whump. John,Ronon, Rodney Friendship

Halloween story, albeit rather late, or, as the case may be, early. Sheppard and McKay are trapped on a world with a malfunctioning Stargate, a monster ... and a mystery. Now complete.

A Wraith queen watches Sheppard suffer. Oneshot. Whump!

Sheppard can’t escape torture even when he’s supposed to be safe on Atlantis.

They're always in the habit of saving each other's lives. It's Rodney's turn now.

Sheppard is held captive and tortured for information. Contains torture, obviously, and lots of Shep whump!

An AU version of what happens after the Return, featuring a strong connection between John and Atlantis.