Dana Scully, a former FBI agent, is now a staff physician at a Catholic hospital; she is treating Christian, a young boy with symptoms similar to Sandhoff disease. FBI agent Mosely Drummy (Alvin "Xzibit" Joiner) approaches Scully for help in locating her former partner, Fox Mulder, who has been in hiding as a fugitive since the events of the series finale. Drummy states that the FBI will call off its manhunt for Mulder if he helps investigate the disappearances of several women in West Virginia, the latest of whom is a young FBI agent named Monica Bannan. Scully agrees and convinces a reluctant Mulder to help.
The duo are taken to Washington, D.C., where Agent Dakota Whitney (Amanda Peet) requests Mulder's expertise with the paranormal as they have been led to a clue, a severed human arm, by Father Joseph Fitzpatrick Crissman (Billy Connolly). He is a former priest defrocked for the child molestation of thirty-seven altar boys, and claims God is sending him visions of the crimes. A second woman, driving home after swimming in a natatorium, is run off the road by a truck driven by Janke Dacyshyn (Callum Keith Rennie), who then abducts her. Father Joe is again recruited for help with the second abducted woman. After a grueling nighttime search in a snow-covered field, he leads the FBI to what turns out to be a frozen burial ground of people and body parts. Analysis of the remains, along with tracking down the recent movements from the second abducted woman's car crash, eventually leads them to Dacyshyn, an organ transporter in Richmond, Virginia, and his husband, Franz Tomczeszyn, who was among the youths Father Joe sexually abused.
During an FBI raid on the organ donor facility where Dacyshyn works, he ends up escaping, leaving Bannan's severed head at the scene. Mulder, who accompanied Whitney on the raid, chases Dacyshyn to a building construction site. Whitney follows, and is killed when Dacyshyn pushes her down an elevator shaft. Scully, seeking a resolution, asks Joe, who has not yet heard of the discovery of Bannan's head, if he senses that she is still alive. He replies that she is. Discouraged but still determined, Mulder decides to investigate the incidents further. He starts by driving Scully's car to Nutter's Feed Store in a small town near the abductions, as the human remains contain acepromazine, an animal tranquilizer. When Dacyshyn coincidentally arrives moments later, Mulder slips out and follows him. Dacyshyn notices him, however, and runs his car off the road. Mulder survives and manages to tail Dacyshyn, who exits his truck after the engine fails, to a small compound in a former barn. Mulder enters, and the commotion caused by a two-headed guard dog brings Dacyshyn out from one of the buildings. The compound is being used by an east-European medical team that has been murdering people and stealing their organs for years. The field where Father Joe had earlier discovered the bodies turned out to be their dumping ground. Mulder enters the building to find that the team has been using the organs and body parts in an attempt to keep Tomczeszyn alive. At that moment, they attempt to place Tomczeszyn's head on the body of the second abducted woman. Mulder tries to save her from the gruesome fate, but a doctor comes from behind and injects him with a tranquilizer. Helpless, Mulder is taken outside to be murdered by Dacyshyn.
Scully, unable to reach Mulder on his cell phone, contacts her old FBI superior, Director Walter Skinner (Mitch Pileggi), for help. They triangulate the phone's location and find Scully's wrecked car, eventually making their way through the snow to find the compound as Mulder is about to be axed by Dacyshyn. Scully attacks him in an ensuing confrontation, incapacitating him, while Skinner breaks up the medical procedure before the young woman is beheaded. Later, Mulder is at home when Scully tells him Father Joe has died. It happened at the same moment, Mulder notes, that Scully disconnected the life support to Tomczeszyn's severed head. Somehow, he surmises, the two men's fates were linked by more than just visions.
Who's head was left behind?
Bannan