Small bodies are excavated from graves outside the Santa's North Pole Workshop in Sacramento (discovered in 7X10). The ghosts of the children rise up out of the earth, look up to the heavens and fade into starlight.

Mulder pores over the tapes found at the crime scene. Scully reports that Ed Truelove confessed to all the children's murders, but did not take responsibility for the disappearance of Amber Lynn LaPierre. Mulder admits to Scully that he had hoped his sister Samantha was among the dead. "I just wanted it to be over," he says. Their conversation is interrupted by the arrival of police psychic Harold Piller who offers to help find Amber Lynn. Piller has previously explained cases where children were transported through spiritual intervention. Although Scully readily dismisses Piller and his theories, Mulder is interested, and notes that Piller's claims match what Kathy Lee Tencate had told him in the prison.

Disapproving of Mulder's blind belief, Scully returns to Washington and shows Special Agent Lewis Schoniger a video of Mulder's 1989 regression hypnotherapy session. As Mulder recalls Samantha's abduction on the tape, the FBI expert points out that Mulder's delusion played into his unconscious hope that his sister was still alive. This caused him to pursue her. The case file reveals that an unsuccessful search for Samantha occurred at the highest levels of government in 1973. Schoniger surmises that Samantha is probably dead, and advises Scully not to dig any deeper. Scully disagrees, saying that someone owes Mulder an explanation because "he deserves closure, like anyone."

Back in Sacramento, Mulder brings Piller to the graves. The psychic senses that Ed Truelove's victims all died while suffering. Walk-ins, however, intervene before anything violent happens to the children. Piller believes that while Amber Lynn was not among the dead children in the graves, she has a connection to Mulder and his missing sister. That night, Piller comes to Mulder's motel room because a "visitor" wants to speak to him. A ghostly vision of the late Mrs. Mulder appears, trying to tell Mulder something. When she quickly disappears, Mulder discredits Piller's abilities, but then realizes that he has unknowingly written the words "April Base" on a piece of paper.

Scully proceeds with her own investigation of Mrs. Mulder's house and finds remnants of burned photos and documents. She calls Mulder to tell him that one of the documents has the Cigarette-Smoking Man's signature calling off the search for Samantha. Mulder discounts the importance of this lead. When Scully gets home later that night, the Cigarette-Smoking Man is waiting for her. He warns her to stop the search for Samantha because he believes she is dead. Although Scully pleads for the truth, CSM contends that Mulder must remain ignorant. It is the only thing that gives him hope. Meanwhile, Mulder and Piller sneak onto the decommissioned April Air Force Base. Piller has a vision of Samantha and other children given tests in train cars. Mulder is at first skeptical, but then finds a child's handprint in the cement outside one of the base houses. Samantha's name is etched underneath. Next to the small hand is another print with the name Jeffrey.

Mulder refutes what the CSM said to Scully, believing that Samantha was returned after her abduction to be raised by CSM and his son, Jeffrey Spender. Scully thinks that Piller is leading Mulder on. The agents confront Piller with the knowledge that he has been institutionalized for schizophrenia and is currently being investigated for the murder of his own son. Piller argues that he only wants to find his son. He tries to prove that he knows Samantha is still out there by taking them back to the base. In the CSM's abandoned house, the three hold hands for a seance to summon the spirits. Ghosts appear around them. A small boy ghost takes Mulder's hand and leads him into an adjoining room. Inside a wall cavity, Mulder finds a diary belonging to Samantha. Later in a diner, he reads the passages to Scully. A fourteen year-old Samantha remembers another family and an older brother, but she seems to think that the doctors performing tests on her have stolen her memories. Her final entry is about running away. Outside, Mulder looks up at the night sky and ponders whether the stars are really comprised of lost souls. He tells Scully that he wonders what his mother was trying to tell him before she died. Late at night, as Mulder sleeps, the ghost of Mrs. Mulder whispers into her son's ear.

The next morning, Scully uncovers a 1979 police report on a runaway who matches Samantha's description. The agents scour old hospital records, finding a "Jane Doe" patient with signs of paranoia. The girl also exhibited strange cuts on her limbs. They go with Piller to the house of Arbutus Ray, the emergency room nurse who signed the patient in. Mulder is hesitant to approach the woman's front door because he somehow senses that he has reached the end of the road. Scully and Piller knock on the door as Mulder waits at the car. Ray does recall the patient and remembers that she had a vision of the girl murdered. A frightened Ray blinked, but realized the girl was sleeping safely. This story matches Bud LaPierre's hallucination. Ray also recounts how a group of men came with the father -- a smoking man -- to take the girl away. When the men opened her locked room, the girl had vanished. Scully turns to Mulder, but he has disappeared. She doesn't see him being led by the same boy from the house at the Air Force base. Mulder walks through a clearing in the woods and sees a group of ghostly children happily playing. Amber Lynn LaPierre is there. Mulder senses that his guide is Harold Piller's son. Suddenly, Samantha runs to Mulder and jumps into her brother's arms. The joyous reunion brings him to tears.

A peaceful Mulder appears out of the darkness, walking towards Scully and Piller. Piller is in denial when Mulder assures him that his son is protected among the Walk-ins. But Scully is concerned about her partner. "I'm fine," he calmly says. "I'm free."