Mulder is running from Krycek in a lab, surrounded by signs warning of radioactivity and toxic substances, when he suddenly finds himself engulfed in a white cloud. As the cloud dissipates, he finds that he's standing outside a house on Echo Lane in Alexandria. And the house is where he and Alex Krycek are living a happy domestic life, complete with two dogs named Chip and Sashi.
Mulder tries to come to terms with the fact that he's somehow landed in a parallel universe, one which diverged from his own the night he did/didn't choose to go to Alex with an offer of comfort and pizza the night of Augustus Cole's death. Subsequent differences in the two worlds include Bill Mulder and Melissa being alive, Scully having a boyfriend (Rubin, a painter), and Alex having a good relationship with his sister Corrine. Also, Alex still works for the bureau. Oh, and Skinner's dead.
While Mulder tries to deal with his new reality, Alex tries to come to terms with the fact that "his" Mulder is gone. Meanwhile, "his" Mulder is stuck in Mulder's universe, trying to figure out how to get home.
When Mulder finally gets back to his own universe, he decides to see if it's really possible to have a romantic relationship with Alex, culminating with a conversation on a boat on an Ontario lake and an encounter in a nearby cabin.
Other things to note:
Mulder eventually determines that Gibson Praise was behind the Mulder-universe switches. Alex as a child had wanted to be Little Joe from Bonanza and had starred in a porn video when he was nineteen. And Scully in the other universe drove a red Saturn, unlike her normal blue Taurus.
Echo Lane, by Louise Wu