My Struggle IV

Following the events of "Ghouli", William has become a fugitive from government agents as he is pivotal to the Cigarette Smoking Man's plans. Reflecting on his difficult childhood, he resolves to find the Cigarette Smoking Man to learn the truth about his nature.

Mulder and Scully receive a call from Monica Reyes, warning them that William has been taken into custody and is being escorted to a government warehouse in Maryland. Scully, who has been struggling with illness and visions of the future by way of her psychic link with William, predicts that he will not be there. Mulder infiltrates the building, but is forced to kill the agents and Mr. Y before he can question them and he finds no trace of William.

Scully identifies a cluster of lottery winners in north-eastern Tennessee, which she believes is a side-effect of William's presence. Mulder picks up the trail but is himself followed by a government agent. William hitches a ride with a truck driver, only to terrify him with his powers. Mulder quits in frustration and instead anticipates that William is heading for Norfolk. Meanwhile, William is picked up by the agent following Mulder.

With the help of Sarah Turner and Brianna Stapleton—the two girls at the center of the "Ghouli" episode—and Sarah's friend Maddy, Mulder finally locates William in a hotel in Norfolk. He convinces William to talk to him as a unit of soldiers, lead by Erika Price, locate the agent's car. The agent is dead, having been torn apart by William. Price's unit descends on William's hotel room and attempt to arrest him. William turns his powers on them, causing them to explode. He nearly loses control and kills Mulder, but regains his composure and flees the scene as the media descends on the hotel.

In a bid to buy Mulder more time, Scully contacts right-wing online webcaster Tad O'Malley and claims that the incident at the hotel was part of the project to release a man-made pathogen developed from an alien virus. Mulder is named as the source for the story, prompting Director Kersh to order Walter Skinner to shut down the X-Files once and for all and to dismiss Mulder and Scully from duty. Scully receives another vision, this time of Mulder's death and pleads with Skinner to help her save him.

Mulder follows William to an abandoned factory on the coast. Scully arrives shortly afterwards and Mulder suggests that they give up trying to find William because he does not want to be found and because they cannot protect him. Scully refuses to back down, pressing Mulder for details when the real Mulder arrives; the Mulder Scully spoke to was William in disguise. As the two chase him through the factory, Skinner realizes that they have been followed by Reyes and the Cigarette Smoking Man. The Cigarette Smoking Man forces the car to run Skinner down. Skinner shoots and seemingly kills Reyes and attempts to outrun the car; Skinner is seemingly crushed between two cars.

The Cigarette Smoking Man confronts William (still under the disguise of Mulder) on the waterfront. William taunts him, challenging him to kill "Mulder". The Cigarette Smoking Man shoots him in the head and he falls into the water, mirroring Scully's vision of Mulder's death. The real Mulder appears, shooting the Cigarette Smoking Man, who realizes that he has killed William. He falls into the water and his body is carried away by the current.

In the aftermath, Mulder and Scully comfort one another. Scully accepts that while William is her biological child, she was never a mother to him and that she and Mulder were never meant to raise him, describing him as an experiment that was implanted in her. Having finally learned the truth about William's parentage, Mulder struggles with the knowledge until Scully reveals that she is pregnant with his child, a seeming impossibility. As the two embrace, William resurfaces from the water elsewhere, conscious and alive.

• "My Struggle IV" at IMDb