Scattered Leaves : Fall by Abracadabra

Scattered Leaves cover

190,000 Words

Scattered Leaves cover
Part of the Seasons series:

Scattered Leaves: This is the third in the Seasons Series; the sequel to Shadows on the Sun. Mulder goes undercover, Scully goes to a conference. Some unanswered questions...

Going Up, Going Down: A smut companion to Scattered Leaves. Yes, I can picture Mulder in almost any setting. And yes, I appreciate his 'backside'.
You do not need to have read the series to read this one.

Outstanding in her Field: A PWP sequel to Going Up/Going Down. Mulder teaches Scully a new game. Not necessary to have read GU/GD, but it helps...

There's still trouble in paradise as Mulder and Scully are sent to Vermont for different reasons.  Mulder is the worst deep undercover agent that the bureau has ever seen as his focus keeps shifting from the job he's there to do. 😀

You might be able to gather from the companion fics included that they do sort out their differences.  This is the final volume of the Seasons Series.