Abductees are being returned - and mysteriously healed...
Richie Szalay is tracking a UFO in Helena, Montana. As he watches, it dumps a naked female figure, and flies off.
The woman is Teresa Hoese, who was abducted the night before Mulder disappeared. Skinner, Doggett and Scully visit Teresa in hospital - she's very ill. Later, in a motel, they question Richie Szalay. His friend Gary was abducted just before Mulder, and Richie decided to investigate the UFO reports in Montana. Doggett has a report that fresh footprints were found where Hoese was dropped - but the prints were from a popular trainer, making Doggett skeptical about Richie's claims to alien sightings.
Scully dreams of Mulder - dead in the UFO. Meanwhile, Jeremiah Smith has assumed the form of Doctor Desai and arranged for Teresa Hoese to be transferred.
Having learnt of Hoese's dissappearance, Doggett calls on Agent Reyes. Reye's specialty is ritualistic crime, and she thinks Mulder may have joined a UFO cult. Perhaps he's waiting to be transported to the mothership, like the Heaven's Gate cultists? Doggett thinks they may find Mulder if they can find the cult leader. Scully is angry at their suggestions.
In a derelict compound, Jeremiah Smith cures Hoese of her injuries, watched by a man called Absalom.
Back at the Montana Hospital, Reyes examines Hoese's X-Rays. When she looks for metallic nasal implants, Scully is amazed - she thought she was a disbeleiver. Reyes likes to keep an open mind, but is sensitive to the energies of the universe and sometimes gets 'feelings' about cases.
Later, Reyes car stalls as she drives. A UFO appears, dropping two more figures. Smith and Absalom take one of the bodies, but the other is Gary - Richie's friend. Reyes gets the number plate of the van used to kidnap the abductee - it's registered to Travis Clayton Moberly, better known as Absalom, the leader of a doomsday cult.
The FBI storm the cult's compound, and arrest Absalom - but Jeremiah Smith escapes. Absalom tells Scullly and Doggett that he has been saving abductees that are deposited on earth - Hoese's recovery supports his story. Examining video of the compound raid, Scully, Reyes and Doggett watch Smith step in to a doorway, then transform into Doggett. Doggett is stunned, and the agents realise that Smith is still in the compound.
Scully identifies Jeremiah Smith by his trainers, and tells him she knows who he is. When she is distracted, he changes from the disguise of a cult follower into his own form. Doggett comes in to tell her they've found Mulder's body in the woods.
Scully recovers Mulder, and races back to the compound hoping that Smith can cure him - but a beam of light from the sky shines into the room where he is being held, and when she enters the room, he is gone.