When Scully returns in a hospital in critical condition, Mulder must try to find out what happened to her and who was responsible before it is too late.

Scully's mother reminisces to Mulder about what Dana was like when she was young as they wait for her gravestone to be ready.

Later, Scully mysteriously turns up in a hospital in critical condition but nobody seems to know how she got there. Mulder storms in demanding to know who brought her here but without luck. Dr. Daly explains to Mulder that she just appeared. When Mulder returns to Scully's side she finds a woman holding a watch over Scully's body. She identifies herself as Melissa, Dana's sister and that she knows what Scully is thinking by "channelling". Suddenly, we see Scully suspended on a river in a dream sequence tied to a cord with Mulder, Melissa and a nurse in the background watching over her.

When Frohike turns up in a suit and a bunch of flowers, Mulder is surprised. Frohike though seems more concerned with Scully's medical charts which seem "weird". He shows the charts to the Lone Gunmen who find that her DNA seems to have been experimented on and that she is dying from what they did to her. Back at the hospital, a man steals Scully's blood when Mulder looks away so Mulder chases him to the basement car park where Mr. X apprehends him and tells him that he is acting like a "schoolboy". Mulder gets away and is about to be beaten to death by the man when X kills him and cleans up the mess saying ruthlessly "You want to see what it takes to find the truth?".

Meanwhile, the Cancer Man informs Skinner to "sit" on Mulder or "they" will. Later, while Mulder is talking with Melissa he receives an anonymous tip of the location of the Cancer Man. Mulder confronts him holding him at gunpoint and when he asks why it was her not him who was taken he replies "I like you. I like her too, that's why she was returned to you."

Back at FBI headquarters, Mulder hands in his resignation and is packing away his desk when Skinner appears not happy with the decision that Mulder has made. He relates a story to Mulder about his horrid time in Vietnam and says that his "resignation is unacceptable".

Mr. X later appears again and tells Mulder that he can arrange an ambush with him to kill the people who abducted Scully by setting a trap. Mulder though is drawn away from killing her captures by Melissa to visit Scully in hospital and returns to find his apartment trashed. Scully later wakens up from her coma much to the joy of Mulder and she tells him that she "had the strength of his beliefs". Mulder returns the cross to Scully. When they all leave, Scully asks one of the nurse who Nurse Owens is (the one who looked over Scully in her dreams) but the nurse replies that she has never worked at the hospital much to the amazed Scully.