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Mulder and Scully, reunited at last, head for an active volcano under a geological study and find a deadly life form that can survive in the searing heat of the crater and is killing the scientists to avoid being discovered.
Scully mysteriously appears in a Washington hospital, alive but in a coma, and Mulder must fight to keep her alive in order to find out what happened to her and who did it to her. Meanwhile, Scully fights her own personal battle as she decides whether to stay or go on to the next world.
While investigating the connection between the abduction of several teenagers and a rural religious cult, Mulder & Scully discover a secret test being performed on the children using the "Purity Control" alien DNA from 'The Erlenmeyer Flask' which leads Mulder to the Crew-Cut Man, Deep Throat's murderer.
The X-Files are no more. Shut down by the FBI, Scully and Mulder have been reassigned. New supernatural events prove that the X-Files investigations are a necessity and Walter Skinner restores them but with a new team, Fox Mulder and Alex Krycek. Mental patient and alien abductee Duane Barry kidnaps Scully and takes her to a mountain where she disappears. Krycek murders Barry. He works for the Cigarette Smoking Man and disappears with his true loyalties revealed. Scully is returned on the edge of death and Mulder faces a critical choice, seek to ambush members of the conspiracy with the help of his new source Mr. X or stay by Scully's bedside. He chooses Scully. Scully recovers and rejoins Mulder on the X-Files.