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Hoping to determine Mulder's whereabouts, Doggett investigates a case that Mulder kept secret from the FBI involving a soul eater, a creature that can consume the sicknesses of others.
A car drives through the rain to a house. The driver emerges and walks to a door marked with a symbol in blood. The driver bursts into the house and the man and woman in the home demand him to leave. A creature that looks somewhat human-like approaches the woman but the driver shoots it three times. He returns to his car and only now is his identity clear: Agent Fox Mulder.
Agent John Doggett is driving towards Squamash, Pennsylvania, while thinking about his task to find Mulder and how Mulder knew he was dying before he disappeared.
John Doggett arrives at the sheriff’s office and meets with Sheriff Kurt Frey. Sheriff Frey informs him that Agent Mulder was there investigating a missing person, Marie Hangemuhl, but that it wasn’t really a missing person case as Marie hadn’t left her home, there was no report, and Mulder only heard about it because of Marie Hangemuhl’s sister contacting him.Doggett and the sheriff go to see the Hangemuhls. Flashing back to Mulder’s interview with the Hangemuhls, we see that Mulder believed Marie Hangemuhl told her sister about something that would come to the house that frightened her. Doggett learns about the Native American legend of a creature in the woods that Mulder seemed to believe in. He noticed plastered over gun shot holes in their home and is told of Marie Hangemuhl’s illness: end stage renal failure.
Agent Doggett returns to Washington, D.C. and searches Mulder’s apartment (feeds the fish too) until he finds a gun Mulder kept hidden under his sink.
Meanwhile a backhoe digs at a stone circle in Squamash while a few townspeople talk about needing to prove something.
Doggett and Assistant Director Skinner talk about the tests on Mulder’s second gun which revealed blood splatter on the barrel. Doggett points out that the gun is missing three rounds and there were three bullet holes in the wall at the Hangemuhl home. No report about the discharge of his weapon was filed though. Mulder’s reports at the time claim he was in D.C. but cell phone records show he was in Pennsylvania. Skinner believes Doggett knows this is his ticket out of the X-Files. Doggett is trying to keep it all quiet though because Scully signed those reports too.
The townspeople of Squamash show up at a cabin in the woods demanding ‘it’ to be sent out. A woman comes out attempting to lie to cover its escape but they spot it and capture him.
Doggett returns to Squamash with Skinner. They ask the Sheriff about the murder of an unidentified transient. Doggett accuses the Sheriff and the Hangemuhls of covering up the murder of the transient committed by Mulder.They travel to the cemetery and Skinner asks why the townspeople would cover up the murder if Mulder did do it as he doesn’t know them. The grave dug up by the backhoe earlier is that of the transient. Doggett and Skinner find the grave empty and Doggett notices that the transient tunneled out of his own coffin.
Sheriff Frey arrives at the Hangemuhl home where the symbol in blood is on the door again. The sheriff says that she better be ready. As the truck with the captive creature arrives, Marie’s husband kisses her goodbye after she strips down. She lies naked on the floor as the hideous creature opens its jaws wide and bites her.
Doggett and Skinner show up and speak with Paul Hangemuhl but the wife is already gone. They can’t help but notice the blood though.
Deep underground, the creature vomits into a person shaped hole in the soil.
Doggett suggests to Skinner that Mulder shot someone all those months ago to protect Marie Hangemuhl; to protect her from the man who was supposed to be in that grave.They contact the Lone Gunmen via video link. Byers explain that the symbol is a medicine wheel from Native American religion. It signifies the totality of life. The circle represents life on into death while the two lines are the two roads that intersect it all, happiness and sorrow. Drawing the symbol on a door is a summons for a person called a soul eater. They consume the sickness of a person. Doggett goes off alone to see the woman in the woods. She was the woman who found the body of it a year earlier and Doggett asks about Mulder. The woman implies that Mulder was trying to save the creature not Hangemuhl. He hears a noise and finds a trap door leading into the underground tunnels. He finds Marie Hangemuhl covered in goo and takes her to the hospital.
Skinner checks in with Doggett who reports that Marie’s kidneys healed spontaneously. Doggett leaves without giving a statement to the sheriff because he knows the man has known all along. He returns to the woman in the woods who watches over the creature. She explains that it looks the way it does because it takes the sickness of others into itself.Doggett learns that Mulder was there to heal himself through the creature but he couldn’t go through with it. Mulder is shown as seeing the thing’s suffering and so he tried to kill it to put it out of its misery. It couldn’t die though and the woman tried to hide the soul eater but the townspeople found out about it because of Doggett’s investigation. They will always want the creature around so they can cure their sicknesses despite the cost to the creature. The soul eater appears in the room. Agent Doggett attempts to take the soul eater away but the townspeople arrive to prevent it. He stands up to them and says he will drive the man out of there. Sheriff Frey shoots Agent Doggett in the back the second he turns around. Frey and the townspeople notice the creature disappeared. They bury Doggett in a shallow grave near the house. Doggett awakens in the tunnels. The woman kneels beside the dead soul eater. She weeps over it, “He took your death. You freed it.”
Doggett is lost about how to start his case report as Skinner shows up. Doggett tells him that he is no closer to finding Mulder than he was months ago. Skinner advises Doggett not to write the report because it would open up a can of worms. Doggett seems willing to accept this as he stares at the medicine wheel symbol. For a brief moment he sees Mulder in the room with him.
- At one point in this episode, Langly, a member of the Lone Gunmen, calls Doggett "Agent Dogbert". This is a reference to a character in the comic strip Dilbert.
- Mulder can be seen frequently in flashbacks throughout this episode, using new footage to represent events of the previous year. No new footage of Scully is used in the entire episode but she does appear in three flashbacks near the start of this episode, using footage that comes from "Within" and "Without", the first two episodes of Season 8.
- David Duchovny as Special Agent Fox Mulder
- Gillian Anderson as Special Agent Dana Scully (credit only)
- Robert Patrick as Special Agent John Doggett