A frantic Mulder enters a hospital in search of Scully, who had suddenly collapsed during the FBI hearing (see previous episode). He finds her unconscious body lying in a bed, her breathing aided by a ventilator. Skinner explains that Scully went into shock and is close to death. When Mulder refuses to cooperate with Skinner, he is escorted to the main FBI building, where he is questioned by Section Chief Scott Blevins and a Senior Agent. But Mulder fails to cooperate with the inquiry and leaves the room.

The Cigarette-Smoking Man meets with the Elder and fellow Syndicate member Quiet Willy. The Elder chastises the Cigarette-Smoking Man for allowing Mulder to escape from the research facility, leaving their project vulnerable to exposure. But the Cigarette-Smoking Man counters that Mulder is much more valuable alive, and plots to assure his loyalty. When the Cigarette-Smoking Man leaves the meeting, the Elder tells Quiet Willy he can "proceed." Scully regains consciousness. She tells Mulder that Skinner is the mole operating from within the Bureau. But Mulder counters that Skinner is withholding Ostelhoff's forensics information, casting doubt on the theory. Their conversation is interrupted by Mrs. Scully and Dana's brother, Bill Jr. Bill blames Mulder-and his cause-for his sister's condition. Shortly thereafter, the Cigarette-Smoking Man approaches Mulder. He informs him that the metallic vial contains a tiny microchip that will cure Scully's illness. Later, Bill Jr. voices grave concern about the chip. But Scully tells Dr. Zuckerman she is willing to give it a try. Meanwhile, Kritschgau testifies before the FBI's investigative panel. He denies knowing the identity of Ostelhoff's killer, states that his own son died earlier that day, and reveals that part of his remuneration is funded by a Congressional lobbying firm called Roush.

In an effort to cement Mulder's trust, the Cigarette-Smoking Man arranges a meeting between Mulder and his sister, Samantha. She reveals that, some time after her abduction, she was taken to a hotel room and told that the Cigarette-Smoking Man is her father. Mulder tells Samantha that their mother is still alive... and that she was lied to by the Cigarette-Smoking Man. Her head spinning with confused emotions, Samantha makes her way back to the Cigarette-Smoking Man's car and disappears into the night. Later, the Cigarette-Smoking Man tells Mulder that Kritschgau deceived him with a host of "beautiful lies." He asks Mulder to quit the Bureau and work for him, but Mulder refuses.

While watching a televised Congressional hearing on biotechnology, the Elder notices Skinner lingering in the audience. He instructs a subordinate to "fix" the problem. Blevins informs Mulder that a ballistics test matched the bullet from Ostelhoff's body to Mulder's service revolver. Blevins also claims that Skinner has been working inside the Bureau with a secret agenda. Mulder refuses to believe the story... and refuses to finger Skinner as a mole during his testimony before the FBI panel (even though such testimony would exonerate himself from wrongdoing).

Mulder takes his place before the FBI panel. Simultaneously, Quiet Willy, rifle in hand, positions himself inside a parking garage opposite the Cigarette-Smoking Man's apartment. Before answering questions regarding his culpability in Ostelhoff's death, Mulder announces the name of the mole who has acted from within FBI: Section Chief Scott Blevins. At almost the same moment, Quiet Willy opens fire, shooting the Cigarette-Smoking Man. Blevins makes his way back to his office. There he encounters the Senior Agent, gun in hand. A shot rings out, and Blevins falls to the ground. The Senior Agent then places the weapon in Blevins' own hand. Shortly thereafter, Skinner tells Mulder that the Cigarette-Smoking Man is dead. Though no body was recovered, the massive loss of blood found inside the apartment leaves no other conclusion. During their conversation, Mulder tells Skinner he guessed as to Blevins' identity as a mole. Skinner confirms that Blevins had been working for a biotechnology company called Roush for four years. Mulder then informs Skinner that Scully's cancer has gone into remission.