Mulder is trapped inside a train car which contains a suspected alien-human hybrid and also a bomb, while Scully pursues the truth about her abduction and the mystery behind the implant in her neck.

Mulder and Scully swap roles as they pursue a man killing priests that claim to have the wounds of Christ. The agents find and must protect a young boy who may be a real stigmatic. While Scully's faith draws her close to the boy, Mulder is convinced of another explanation.

Widespread panic is caused in a small community after numerous deaths are linked to killer cockroaches, and a government agricultural agency is discovered to have set up a secret experiment involving insects.

A serial killer is captured after a three year manhunt, and he claims an evil spirit is responsible for the crimes. When the killings continue as he sits in jail, Mulder's battle with a former colleague gets more heated when he suggests that something more paranormal may be involved.

Mulder pursues Krycek (unaware of the alien that has taken over his body) to get back the DAT tape containing the MJ documents. Meanwhile, the shooting of A.D. Skinner uncovers evidence that could lead Scully to her sister's murderer.

The unearthing of an ancient Ecuadorian Amaru urn and its removal to America despite protests leads to a series of deaths linked to a shaman spirit released by the urn.

Filmed in glorious black and white with a comic book feel to it, this is a modern retelling of Frankenstein as Mulder and Scully get caught up in a town where the residents live on Jerry Springer episodes and fear a two-faced monster who has been impregnating the women.