The Cigarette-Smoking Man burned the train car Mulder was trapped in. Everyone believed Mulder to be dead - except for Scully. She was on mandatory leave until the matter of her insubordination was cleared out. Meanwhile, she enlisted Skinner's help in clearing Mulder's name from murdering his father, which Skinner refused. Back in New Mexico, where Mulder had officially "disappeared", Albert Hosteen and his tribe discovered Mulder's seriously injuried body, and engaged him in a ritual called The Blessing Way in order to save his life. Back in Washington, Scully discovered that she had a computer chip planted in the back of her neck, and underwent a repression hypnosis with her sister's insistance. During the hypnosis, she saw repressed lights, alarms and men around her - memories believed to have originated from her 3-month-long abduction period. Then, Scully attended Bill Mulder's funeral, and the Well-Manicured Man warned Scully of assasins coming after her. Pumped with paranoia, Scully ran into Skinner, who was waiting for her outside her apartment. They went to Mulder's apartment to talk, while Scully suspected Skinner might be the assassin, and the two held each other at gun point when someone approached the front door......

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