S1E19 · Shapes

FBI agents Dana Scully and Fox Mulder travel to Browning, Montana, to investigate the killing of a Native American man, Joseph Goodensnake, by local rancher Jim Parker. The killing appears to be motivated by a dispute over the ownership of a tract of land, although Parker claims that he fired on a monstrous animal rather than a human. Parker's son, Lyle, bears scars that lend credence to the story.

At the scene of the shooting, Scully reasons that at the short range from which Goodensnake was shot, it would have been impossible to mistake him for an animal. However, Mulder finds tracks leading to the area that appear to change from human to something more animal in nature. Scully dismisses this but finds a large section of shed human skin nearby. She believes that the Parkers knowingly killed Goodensnake, but knows that they could not have skinned him since no signs of such injury were found on the body.

The investigation is complicated by the hostility Mulder and Scully face from the Native American population, stemming from their experience with the FBI during the 1973 Wounded Knee incident. Goodensnake's sister Gwen is also bitter that her neighbors are too frightened of native legends to confront his death. The local sheriff, Charles Tskany, permits Scully to make a cursory examination of Goodensnake's body but forbids a full autopsy. They discover that he had elongated canines, similar to those of an animal, and bears long-healed scars similar to Lyle's.

Mulder tells Scully of a similar incident in the area forty years previously, which was investigated by J. Edgar Hoover and became the FBI's first X-File case. As the agents watch Goodensnake's body being cremated in a traditional ceremony, Mulder shares with Scully his belief that the culprits in both the current case and Hoover's investigation are werewolves. Scully dismisses this theory and instead credits the belief to clinical lycanthropy. Parker is subsequently ripped apart by an unseen animal outside his home, and Lyle is found naked and unconscious a few hundred yards away.

Ish, one of the elders of the reservation, explains to Mulder the legend of the manitou, a shape-shifter that can pass to a new host, through a bite or upon the death of the original host. Ish believes he had seen the creature in his youth but was too frightened to confront it. He says it happens every eight years to someone in the region, and that it has been that long since the last sighting of a possible manitou.

Mulder calls the medical examiner, who tells him that Scully has taken Lyle back to the ranch, and Parker's blood type was found in Lyle's stomach. Mulder and Tskany hurry to the ranch. After firing on the creature, which escapes unharmed, Mulder finds Scully hiding upstairs. They search for the creature, which is shot by Tskany as it lunges to attack them. Scully expresses disbelief on seeing Lyle's body, believing they were attacked by a captive cougar; Tskany replies that the cougar is still in its cage. As the agents leave, they learn that Gwen has left town, while Ish cryptically warns Mulder, "FBI... See you in about... eight years". As Mulder and Scully drive away, a wolf is heard howling in the forest.