S7E11 · Closure

For the first five seasons of the series, FBI federal agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) sought to gain understanding about the disappearance of Mulder's sister, Samantha, who was abducted when Mulder was 12 years old. In the previous episode, " Sein und Zeit ", Mulder and Scully tracked down a serial killer who targeted children. While investigating the case, Mulder began to get emotionally involved, due to the similarities with his sister's disappearance.

Mulder and Scully aid the Sacramento Police in the investigation of a brutal murder committed by Truelove, the owner of the Santa Village. As the remains of more children are discovered, he admits killing twenty-four children, but denies murdering Amber Lynn LaPierre, who disappeared from her home in the previous episode. Mulder is approached by psychic Harold Piller, who tells Mulder that he has helped law enforcement across the world, and has proved in various cases that children had been taken by " walk-ins ", beings composed of starlight. Piller believes that walk-ins save children who suffer terrible fates.

Scully becomes worried about Piller's influence over Mulder. The agents return to Washington, D.C., where Mulder keeps searching for evidence in the case. Meanwhile, Piller gets a vision of Mulder's mother, who recently died by suicide, leading Mulder to April Air Force Base. Scully finds evidence that Samantha's disappearance is linked to The Smoking Man (William B. Davis); when she returns to her apartment, she finds him waiting for her. He tells her that he had called off the search for Mulder's sister when she vanished because he knew she was dead.

When Mulder returns to April Air Force Base, he uncovers proof that Samantha lived with the Smoking Man along with his son, Jeffrey Spender, and that she was forced to undergo painful tests. Scully finds a 1979 police report of a girl matching Samantha's description, and learns that she was taken to a hospital emergency room. She and Mulder find the nurse who treated her, and the nurse describes how Samantha disappeared the same way as Amber, without a trace. Mulder later walks through the forest and has a vision of Samantha along with the spirits of other children, including Amber Lynn.

Upon telling Scully and Piller of his vision, Piller reacts badly upon hearing that his son is dead, while Mulder accepts that his sister is dead and in a better place. When Scully comforts Mulder and asks if he is all right, he responds with a choked "I'm fine. I'm free."