Exploring Desires by K Benton

Exploring Desires cover

100,000 Words

Exploring Desires cover

When Mulder and Scully work with a new agent, his entry into their lives causes months of intense angst for everyone involved.

Content Warning: non-consensual sexual situations, deviant sexual situations, physical control, coercive control, violence. Some scenes are marked, including a court scene which may be especially distressing for rape survivors.

This starts with Scully dating another agent before discovering it's Mulder she really wants. From there things get dark.  Unless you're particularly sensitive, you shouldn't let the content warning put you off - just be prepared to hurt a little.