FBI special agent Fox Mulder (David Duchovny) is currently missing, having been abducted by aliens in the seventh season finale, "Requiem." His partner Dana Scully (Gillian Anderson) has been working with Agent John Doggett (Robert Patrick) in order to locate him. Shortly after Mulder was abducted, Scully and Doggett learned that he had been suffering from a brain tumor and was nearing his demise. After a false lead in the Arizona desert early in the year, Doggett has been assigned to the X-Files division, but he has continued his search for Mulder, despite a lack of definite leads.
A man—whose face is hidden from the camera—drives up to and enters a house, which has an ominous symbol drawn in blood on the door. When he's inside, a humanoid creature approaches a woman but the mysterious man shoots the creature three times. As he returns to his car his identity is finally revealed: Fox Mulder.
Doggett investigates a possible lead into Mulder's disappearance in Squamash, Pennsylvania. Apparently, in the spring of 2000, Mulder visited the town searching for something to cure his terminal brain disease that he received via exposure to an alien artifact. Doggett is informed by the local sheriff (Michael McGrady) that Mulder was investigating a case involving Marie Hangemuhl (Natalie Radford). Marie was told by her sister about a Native American legend of a creature that lives in the woods. While interrogating the Hangemuhls in the present, Doggett learns that Marie is suffering from terminal renal failure. As he is leaving, he also notices plastered-over gunshot holes in their wall. Later, at Mulder's apartment, Doggett finds a gun he kept hidden under his sink. Meanwhile, in Squamash, a backhoe digs at a stone circle located in the town cemetery. Later that night, the townsfolk show up at a cabin in the woods, demanding to a rustic woman (Caroline Lagerfelt) living there that "it" be sent out. A creature attempts to escape, but it is captured.
Doggett and Walter Skinner (Mitch Pileggi) return to Squamash and ask the sheriff about the murder of an unidentified transient, who Doggett believes that the transient was killed by Mulder. Doggett and Skinner travel to the cemetery and discover that the grave dug up by the backhoe earlier is that of the transient. The two find the casket empty, but Doggett notices that the transient dug himself out of his own coffin. The sheriff arrives with the creature—revealed to be a soul eater, which subsists off human disease—at the Hangemuhl home, where the symbol in blood is on the door again. The hideous creature opens its jaws wide and bites Marie. Doggett suggests to Skinner that Mulder shot someone to protect her from the man who was supposed to be in that grave. Meanwhile, deep underground, the creature vomits what appears to be the visceral remains of Marie into a person-shaped mold in the soil.
Doggett goes off alone to see the woman who guarded the creature in the woods. The woman implies that Mulder, feeling sorry for the creature, was trying to euthanize it, not save Marie. Doggett hears a noise and finds a trap door leading into the tunnels. Underground, he finds Marie and takes her to the hospital. He reports to Skinner that her kidneys have healed spontaneously. Doggett returns to the woman who watches over the creature; after recoiling at its ugliness, the woman explains that it looks the way it does because it takes the sickness of others into itself, while healing them in the process. Doggett decides to take the creature away from society, which only uses it. However, Doggett is shot and killed in a scuffle with the sheriff and is promptly buried. Later, Doggett awakens in the tunnels. In the dark corner of the cavern, the woman weeps beside the dead soul eater. She reveals that, by eating Doggett's death, it has finally been allowed to die.
Back at FBI Headquarters, Doggett is struggling to write his report. When Skinner checks in on him, he encourages Doggett to not submit a report, as it would contradict Mulder's earlier report and damage his, Scully's, and Doggett's own reputation. Doggett protests that Scully had no knowledge of the events, but Skinner reminds him that it would take months to clear her name, and that it is enough that the two of them know the truth about what happened.
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