Six years after the events of The X-Files series finale, former FBIagent Doctor Dana Scully is now a staff physician at Our Lady ofSorrows, a Catholic hospital, and treating a boy named Christian whohas Sandhoff disease, a terminal brain condition. FBI agent Drummyarrives to ask Scully's help in locating Fox Mulder, the fugitiveformer head of the X-Files division, and says they will call off itsmanhunt for him if he will help investigate the disappearances ofseveral women, including young FBI agent Monica Banan. Scully agreesand convinces Mulder who is living in a nearby small home, bearded andclipping newspaper articles about the paranormal to help, despiteMulder's initial misgivings that this is an FBI trick to capture him.

The duo is taken to Washington, D.C., where Agent Dakota Whitney wantsMulder's expertise with the paranormal as they have been led to a clueby Father Joseph (Joe) Fitzgerald Crissman (Billy Connolly), a priestdefrocked for pedophilia who claims God is sending him visions of thecrimes. Mulder wants to believe the man, but Scully is disgusted byFather Joe's past and disregards his "visions".
Whitney andDrummy take Father Joe and Mulder to the kidnapped Banan's home, wherethe former priest overcomes the others' skepticism when, in anguish andon his knees in pain, he begins bleeding from the eyes. A second woman,driving home after swimming in a natatorium, is run off the road byJanke Dacyshyn (Callum Keith Rennie), a snowplow driver who thensmashes the window of her wrecked car and abducts her.