At a remote cattle ranch in the Montana countryside, Jim Parker and his son Lyle are attacked by a ferocious, wolf-like beast. Hampered by darkness and a raging thunderstorm, Jim fires his shotgun at the creature and kills it. When he examines the body, Jim discovers he actually killed a Native American man known as Joseph Goodensnake.

Mulder convinces Scully to aid him with the investigation, which at first glance does not appear to be related to the supernatural, but rather, a tragic accident. They interview Jim Parker, who explains that someone-or something-had been mutilating his cattle. He insists that he shot a wolf-like beast with his gun-not Goodensnake. Mulder's curiosity is piqued when he discovers a piece of translucent skin where Goodensnake's body had been recovered.

The agents travel to Trego Indian Reservation, where Sheriff Charlie Tskany allows them to examine Goodensnake's body. They discover that Goodensnake's front teeth are abnormally-long, not unlike that of a wild animal. But the sheriff refuses Scully's request to perform a detailed autopsy, citing Native American burial rituals.

As members of the tribe burn Goodensnake's body at a burial ground, Mulder explains to Scully that the oldest X-File on record was created by J. Edgar Hoover. It involved a series of murders that occurred in the United States during World War II in which victims were mauled to death by what police assumed to be a wild animal. An animal was tracked and killed by police, but when they retrieved the carcass, they found only the body of a man. Scully insists it is physically impossible for a human to change form.

Lyle Parker arrives at the burial grounds to offer his condolences to Goodensnake's sister, Gwen. She becomes distraught and insists that he leave.

Not long after the cremation, Mulder and Scully discover Jim Parker's mutilated corpse at his ranch. They also find Lyle Parker, lying naked in the mud nearby. Scully transports Lyle to the hospital for treatment while Mulder and Sheriff Tskany continue the investigation.

Tskany takes Mulder to the home of Ish, an elderly mystic Native American. Ish explains that the attacks that occurred during World War II were the result of a Manitou, an evil spirit capable of changing a man into a beast. Tskany speculates that because the power is passed through bloodlines, Gwen too may be a shape-shifter, and she may have killed Jim Parker to avenge her brother's death. But when Gwen is interviewed, she claims she saw a wolf-like creature attack and kill Jim Parker.

Mulder and Tskany realize that Lyle may have contracted the shape-shifting power after he was mauled by the beast. They race back to the Parker ranch, where Mulder rescues Scully by shooting and killing a wolf-creature. Moments later, the creature reverts to Lyle's form.