He is the Master of His Fate, She is the Captain of Her Soul by ScullyLikesScience

946,000 words & counting

Book Cover: He is the Master of His Fate, She is the Captain of Her Soul by ScullyLikesScience

The story begins during the final events of “The Sixth Extinction II: Amor Fati.” It then chronicles a canon-compliant progression of Mulder and Scully's relationship throughout Season 7, including the beginning of their love affair, and on through Seasons 8 & 9.

The story will conclude post-IWTB, and may or may not incorporate Season 10 & 11 storylines.

 

This is the first of the "current classics" I want to include here. 

With works on AO3, I'll only link to the story in its original location, because it can be downloaded from there in a number of formats.  Plus, this one is still being added to.  It follows canon, so it's not a WIP as such.