Krycek played the role of Trickster in this episode. He does a lot of things that are annoying, and even a little mean...but he doesn't do any real harm. He tortures Skinner with the nanobots, just to get his attention, and plays with him a little. He offers a vaccine to cure the seriously ill Mulder - if Skinner makes sure Scully's baby never comes to term. However, I don't think Krycek ever seriously expected Skinner to agree to that. He doesn't threaten Skinner with the nanobots when he refuses, nor kill him - though he could. Later, he taunts Doggett in the parking garage, offering the vaccine, then dropping it, to shatter on the floor when Dogget moves to get it.
Despite these pranks, it's possible that Krycek is really the one who saved Mulder. The explanation offered is that when Skinner, in despair, disconnected the life support, Mulder was cured. Because the life support had been supporting the virus. That seems far-fetched, to me. I think Krycek gave Mulder the vaccine. He was alone with Mulder for awhile. And shortly afterward, Mulder got better.
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