I just watched it (going through the mythology episodes). Mulder had what Scully "strongly believed" was the alien virus. Doggett failed to get the vaccine from Krycek so Skully treated him with "antivirals" and it worked.
Did Scully cure Mulder of the alien virus without the vaccine (that the syndicate was working on for roughly 50 years)?
Also : How is it that, previously, the alien virus made a scary alien grow and burst out of someone's chest cavity, but this one made Billy Miles shed his skin and then appeared normal?