Mulder, driven by a need to understand what really happened to his father, decides to head back to the silo (Piper Maru/Apocrypha) to find Alex Krycek, who he's convinced he heard crying out when he and Scully were there.
!CW: consent is freely given, but under circumstances that could be considered duress.
As stated in the author's notes, her wish was to explore the M/S relationship in a way that it "gives them a kind of mystical strength, one that frightens the powers that be, one that could actually help them in their quest for the truth"
Whilst their first time is under less than perfect circumstances, it connects them in a special way that continues through the challenges they face in the rest of the stories. I do have a special love for an early connection between our agents, and this one feels right for them.