The episode opens with an introduction by the Cigarette Smoking Man (William B. Davis), in which his full name is revealed as Carl Gerhard Busch Spender.
Dana Scully (Gillian Anderson) wakes up in the hospital after having a seizure, now realizing the apparent invasion was a vision and hasn't actually happened yet. She tries to warn Fox Mulder (David Duchovny) about the plague. Mulder initially presumes Scully’s ramblings are a product of her illness, but leaves the hospital to investigate. Elsewhere, Agent Jeffrey Spender is chased down and hit by a car in a parking garage. Spender hides behind a door of an apartment building as his would-be assailant demands the whereabouts of a boy. Spender calls Mulder and the Smoking Man intercepts the call, revealing that he is in a room with Monica Reyes. A car chase soon unfolds in which Mulder is able to evade another man.
Spender later appears at Scully’s bedside, revealing that someone is looking for William. He first balks at telling her the location of her son, revealing only the name of the family that adopted him - Van De Kamp. Mulder tails a henchman who he believes will take him to the Smoking Man, but he arrives somewhere else with mysterious conspirators; Mr. Y (A.C. Peterson) and Erika Price (Barbara Hershey). The pair says they were once part of the Syndicate, but have their own agenda involving the colonization of space. They try to negotiate with Mulder into turning over his son, but Mulder refuses.
Walter Skinner (Mitch Pileggi) tries to meet with Scully, but can't find her. As he goes to his car, he is met inside by the Smoking Man and Reyes, the latter holding him at gunpoint. The Smoking Man asks Skinner to turn his back on humanity in return for immunity from the Spartan virus, but Skinner is very hesitant. Meanwhile, Scully tries to leave the hospital but her seizures return, causing her to crash her car. She is rescued by Agent Einstein and Agent Miller, and is readmitted to the hospital. Both agents leave the room. An assassin sent by Mr. Y and Erika enters and tries to suffocate Scully, but Mulder steps in and saves her by slicing the assassin's neck.
After Mulder kills the assassin, Scully says that she doesn’t think the Smoking Man sent him. She then reveals her visions are from William. As Skinner comes in, Mulder confronts him since he smells like smoke. In a flashback to when Skinner was in the car with the Smoking Man, the latter reveals in a further flashback that he, not Mulder, artificially impregnated Scully. The final scene (out of focus) shows a teen, presumably William, having seizures.
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