One day, the Gunmen just disappeared.
This was ML's wish for how the X-Files would end.
A Season 9 Fic with William in it. Not the usual fic you'll find uploaded here but there was a request in a facebook group for Mulder secretly meeting with Scully while he was on the run in Season 9 and this one kind of fitted the bill. This includes the original story "Abandoned" plus the subsequent story, "Apart" which details the events of Season 9 from Mulder's POV.
It's been so long since I've read these that I can't think of tags to add, sorry.