This is kind of cool -- I think I'd write it as a more-or-less straightforward political story, set in an around Mulder's search for an explanation for his sister's mysterious disappearance. So the Consortium is actually a Loyalist organization working secretly within the Revolutionary movement to undercut and betray it -- and Mulder and Scully are (of course!) revolutionaries, but Mulder is torn between his political ideals and his need to investigate the Consortium, which he is sure is responsible for Samantha's fate! Cue a great deal of soul-searching and angst.

Scully, in this universe, really is a doctor: one of those over-educated New England women, and her family has no idea what to do with her, or with her strange attachment to Mulder. Mulder, of course, is far too involved in his own problems to worry about the way she's transgressing gender roles.

In this universe, Krycek is French.