Mulder and Scully are abducted and when they are returned, things have changed.
After being missing for two months, when they were found, conclusions were leapt to and evidence tampered with. Just another day on the X-Files.... On top of that, some ardent loving is walked in on, and there's some video evidence gleefully provided by some voyeuristic members of the consortium. It's only glancingly mytharc.
Content warning: there is dubcon involved in this (they were drugged but otherwise willing).