Despite Mulder's objection that it is still too soon to give up hope, Margaret Scully orders a gravestone for her missing daughter, Dana. Not long afterward, Dana's comatose body mysteriously appears at a local hospital. She is hooked to a life support system and her condition is deemed critical. There are no records indicating how she arrived at the hospital or who brought her there. Mulder is furious. A doctor reveals that Dana's living will specifically requests termination of life support should such a situation develop.

Melissa Scully visits the hospital. She claims that, through channeling, she can communicate with her sister. Dana also receives a visit from Frohike, one of the Lone Gunman. Frohike and his colleagues discover that Dana's DNA exhibits signs of genetic tampering. They conclude that with her immune system decimated, Dana does not have long to live.

When Mulder returns to the hospital, he sees a mysterious man steal a vial containing Dana's blood sample. Mulder gives chase. A fight ensues between the two men. Suddenly, X emerges from the shadows and shoots the mysterious man. Mulder is shocked at the senselessness of the killing. He does, however, recover the blood sample. Soon after, the Scullys honor Dana's wish and the life support system is disconnected.

Mulder approaches Skinner and demands access to the mysterious Cigarette-Smoking Man, convinced he is responsible for the cover-up. His request is denied. Some time later, at the hospital, a mysterious woman leaves behind a pack of cigarettes containing the Smoking Man's address. Mulder secretly enters the Smoking Man's apartment and puts a gun to his head. The Smoking Man reminds Mulder that if he dies, he takes all the secrets with him. Realizing he has arrived at a dead end, Mulder turns in his resignation. Skinner refuses to accept it.

Later, Mulder is approached by X and given information that an illegal search by government operatives will occur at his apartment. Mulder is instructed to kill the intruders and claim self-defense. As Mulder waits in the darkness for the agents, Melissa appears at his door. She tells him that Dana's condition is deteriorating, and that now more than ever, Dana needs him at her side. Mulder visits Scully's bedside and gives her words of encouragement. When Mulder returns to his apartment, he finds that it has been ransacked.

The next day, Mulder visits the hospital where Dana has regained consciousness. "I had the strength of your beliefs," she tells him.