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Scully and her Catholic faith must confront the loss of her daughter Emily when she is asked to help a family whose adopted daughter was found dead in a position that looked like she was struck down by God himself.
Agents Mulder and Scully investigate a murder that seems to have been committed by a blind woman, but Mulder suspects that her involvement is not what it seems. The agents soon find out that the blind woman some how has the ability to look through the eyes of the killer and get to the crime seen first.
Scully fears that Mulder has gone to the other side when she sees him assisting a federal suspect escape custody. In truth he has infiltrated a terrorist group testing a deadly biological weapon that can eat through a person's flesh.
Scully is suffering from cancer while Mulder is doubtful that aliens exist. The agents fake Mulder's death in an effort to discover which members of the FBI they can trust before individually searching for an answer to Scully's cancer. Her condition worsens, however, and she is hospitalized before Mulder is offered an alleged cure by the Cigarette-Smoking Man. The man also brings Mulder a woman who claims to be his sister, Samantha, although she leaves with the Cigarette-Smoking Man shortly thereafter. When the man offers Mulder a deal to join him, Mulder immediately refuses. He returns to the FBI Headquarters, where he announces that Section Chief Scott Blevins is responsible for Scully's cancer. Both the Section Chief and the Cigarette-Smoking Man are shot. Scully begins to recover and eventually resumes her work on the X-files with Mulder. While staying with her family at Christmas time, she learns that the adopted daughter of a deceased woman is apparently her own child.