Scully's mother tells Fox Mulder (David Duchovny) about when Dana (Gillian Anderson) shot a snake with her brothers as a child and regretted what she did afterwards. A young man walks in, showing them Scully's gravestone. Scully later turns up mysteriously at the hospital in a coma. An out of control Mulder is thrown out by security but later calms down and meets with Dr. Daly, who says no one knows how she got there or whats wrong with her. He tells Mulder and Mrs. Scully that she has a living will that dictates she be taken off of life support when she reaches a certain level. At Scully's bedside Mulder meets her older sister, Melissa. A sequence shows Scully sitting in a boat, attached by rope to a dock where Mulder and Melissa stand. Frohike visits Scully and sneaks out a chart on her, that the Lone Gunmen investigate. The newest Lone Gunman, known as 'The Thinker' assists, and tells them that Scully's blood contains branched DNA that may have been used for identification but now is inactive and nothing more than a poisonous waste product in her system. The mysterious Nurse Owens visits Scully at her bedside. Later Mulder visits Scully while another nurse takes her blood. When distracted, a mysterious man steals Scully's blood sample and runs. Mulder chases him down to the parking lot where he is confronted by X, who demands that he stop pursuing what happened to Scully and let her die. He then executes the man who stole her blood. When Assistant Director Walter Skinner calls Mulder to his office regarding the incident, Mulder denies any involvement and claims that the Cigarette Smoking Man is responsible for what happened to Scully. Mulder, calling him "Cancer Man" demands to know where he is but Skinner refuses to provide him with that information. In another vision Scully sits on a table and is visited by her deceased father. Mulder, sitting with Melissa in the hospital cafetaria is asked by a woman for change for the cigarette machine. When she says that a pack of Morleys is already there and leaves, Mulder opens it and finds the Cigarette Smoking Man's address inside. Mulder bursts into the Cigarette Smoking Man's home and holds him at gunpoint, demanding to know why Scully was taken instead of him. The Cigarette Smoking Man claims he likes the both of them, which is why she was returned. Telling Mulder that he'll never know the truth if he kills him, Mulder decides not to kill him. Mulder returns to FBI headquarters and types out a resignation letter that he hands into Skinner. Skinner comes down later, telling him of an experience when he was in Vietnam where he had an out of body experience. Skinner refuses to accept Mulder's resignation and Mulder realizes that he was the once who provided him with the Cigarette Smoking Man's location. Heading to the parking garage, Mulder is met by X, telling him that he'll have a chance for revenge that night when men, believing him to have information on Scully, will be appearing at his apartment. Mulder waits with his gun at his apartment when Melissa arrives. When Mulder refuses to leave to see Scully Melissa argues with him over his negative attitude. Mulder decides to head to Scully's bedside after all. Returning home to find his apartment trashed, Mulder sits on the floor and cries. The next day, Scully awakens. Mulder is called to the hospital and sees her, giving her a Super Bowl video. Scully tells him she doesn't remember anything after being kidnapped by Duane Barry. Later Scully asks one of the nurses if she can see Nurse Owens, as she wants to give her cross necklace to her. The nurse tells Scully that no nurse named Owens works at the hospital.