Sheppard captured by Koyla; McKay builds nucelar bomb

I'm looking for a long story, at least six years old. The scene that's sticking with me is: Sheppard has been capturd by Koyla, who is broadcasting his torture to Atlantis (he stabs Sheppard through the wrist with a pronged fork). McKay threatens Koyla with a nuclear bomb, which he then builds and pushes through the Stargate

At the end, when Sheppard comes back through the Stargate, McKay hugs him and Sheppard says somethign along the lines of "I think my boyfriend just outed me".

Is it the same story as the one where Elizabeth has been poisoned, is in stasis, and MacKay is in charge of Atlantis? I don't know.