A strange creature is killing people in a small town, but the history of the crimes reveals a missing person...
Burley, Idaho - an undertaker and his wife are killed by a strange bat-like creature. Reviewing the case, Scully notices that the bite marks on the bodies are human.
Scully and Doggett make contact with the local detective, Abbott, who shows them the crime scene. They see strange, webbed footprints, and discover two regurgitated human fingers in the attic. After performing autopsies on the victims, Scully concludes that the couple were killed by some kind of bat.
Doggett shows her a 1956 newspaper report about three hunters who shot and killed a bat-like creature - soon after the autopsy on the creature, the local coroner was disembowelled, and five more people killed in similar circumstances.
Back in the present, another elderly woman is killed. Investigating Scully and Abbott find scratch marks in her attic, as if someone, or something, has forced entry. Looking through the victim's photo album, Scully discovers that the woman's daughter, Ariel, was the burned body that had been pulled from the river the previous week, having been missing for forty years. Scully thinks there might be a connection with the 1956 killings.
Doggett interviews Swanny Swanson at the Manhattan, Montana Press Telegram offices. He recalls the shooting of the bat creature, and wonders if it could have had a mate. Back in Idaho, Abbott exhumes Ariel's body - which has been partly dug up by something already. Alone in the graveyard, he is killed by the bat monster.
Scully performs an autopsy on Ariel, discovering that she died of natural causes, and was burned after her death. All of the recent victims have had contact with the burnt corpse, which means a man called Myron Stefaniuk could be the next victim.
The Agents warn Myron, who confirms Doggett's hunch that his brother, Ernie Stefaniuk, was one of the hunters killed by the bat creature years before. Myron asks to be left in peace, but the suspicious Agents stake out his house. Late that night, they follow him to the river where he floats a crate out into the water. On the opposite shore, someone swaddled from head to foot collects the crate, but is surprised by Scully and Doggett in a boat.
The man, whose face is horribly disfigured by bite marks, turns out to be Ernie Stefaniuk, who has been living as a hermit on an island for forty-four years. The surrounding water has prevented the bat creature from seeking out his scent, which is also why he burnt the body of his wife Ariel - so the creature would not smell him on her.
Doggett heads back to find Myron, but is attacked by the creature and escapes by jumping into the river - both Scully and Doggett are in danger, as they now carry Ernie's scent. Back in the cabin, one of Ernie's alarms triggers - the creature is on the roof. Scully shoots it through the roof, and goes outside to find the body. The bat creature comes down the chimney to attack Ernie, but Scully and Doggett open fire - it flies off into the night.
Back at FBI HQ, Scully wonders if the creature will come after them - Doggett is convinced they shot it. As she leaves the office, Scully puts Mulder's name plate away in a drawer.