A woman named Marty seduces a businessman at a trendy nightclub. The couple go to a motel and have sex. Shortly thereafter the businessman begins convulsing and dies. Before Marty leaves the motel, her physique changes and she metamorphoses into a man.

Mulder and Scully are assigned to investigate the case. Mulder links the death to a series of others in which victims died in the throes of passion. Medical tests reveal large amounts of pheromones in the victim's blood. He also links two of the murders to a remote town in Massachusetts inhabited by The Kindred-a sect of religious isolationists famous for their abstinence and pure Christian beliefs.

The agents travel to the rural village, where sect members allow them access to their community only after they relinquish their guns. As Mulder and Scully dine with The Kindred, Brother Aaron suddenly begins choking. Scully is forbidden by the other sect members from aiding Brother Aaron, and he is led away.

The agents perform some clandestine investigating during the night. They are intrigued by activity emanating from a cellar beneath a barn. Mulder makes his way inside and watches a ceremony centering around Brother Aaron's body. In his effort to keep his presence a secret, Mulder becomes trapped inside a crypt where Aaron's body is entombed in a strange, membranous substance. He watches as Brother Aaron's body begins transforming into a woman.

Scully, meanwhile, has been pulled aside by Brother Andrew, a handsome sect member who possesses a mysterious hypnotic power. Andrew tells Scully he believes the murders were committed by Brother Martin. But before he reveals how Martin killed, Andrew places Scully in a trance and begins kissing her. Mulder breaks out of the crypt and rescues Scully before Andrew takes further advantage of her.

Mulder and Scully are permitted to leave the town. They receive a break in the case when one of Martin's intended victims escapes harmed, but alive. He describes how his attacker changed gender right before his eyes.

Police track Marty to a hotel after he/she orders food using a victim's credit card. Mulder and Scully raid a hotel room and encounter Marty and his latest victim. Marty flees but agents give chase. Before they can apprehend Marty, however, he/she is surrounded by fellow Kindred members and dragged into the darkness.

Scully, Mulder and other FBI agents raid the village where the sect lives. But they find the village completely deserted. The only clue left is a distinctive crop circle near the barn.