It's been a few years since the old men have died - three years since Mulder's seen Krycek. And Krycek's life hasn't been good in that time. He's living homeless for the past year on the street near Mulder's place, and as the story opens it's January and Krycek is expecting to die on the streets. But Mulder comes across him and takes him in.
So Mulder takes care of Alex, cleaning him up and trimming his hair, and the two do the usual rehash of old times and old wounds. Alex reveals that he killed William Mulder and that William had been responsible for Alex's parents' deaths. Mulder has a few angsty seconds of remembering a time in the past when he and Alex had sex, and when he thought Alex could be someone special to him.
It's when the story moves past this that it gets really good. Mulder arranges, through the Lone Gunmen, to meet with someone who can help Alex. As a result, Alex ends up working for a high-end security firm. And while Mulder realizes that he's still in love with Alex, Alex realizes that he's got to do this right. So he moves out of Mulder's apartment and eventually asks Mulder out on a "date" - complete with both of them concerned about what to wear.
The two are dating (movies, dinners, baseball games) for a few months when Krycek is shot while on duty (guarding the Iraqi delegation). Mulder (along with Scully) rush to the hospital, and although Alex has been shot through a Kevlar vest, he'll eventually be fine. He's also getting a reward from the security firm. He wants to use the money to buy a red convertible. Unfortunately, the car-shopping experience highlights the issues with his prosthetic arm. Alex takes out his frustration by terrorizing the salesman.
He does end up getting a car, however - one he shows up with when he arrives to pick Mulder up for a week at a secluded beach house. It's at the beach house that they declare their love, sleep together, and start talking about forever together.
The End of the Cold War, by Kadru