At the start of the episode, we see mourners paying their respects to Isaac Luria, a Hasidic Jew brutally murdered by three hate-mongers. When everyone has left and night has fallen, we see a shadowy figure enter the cemetery and sculpture a man sized model out of the mud.

Mulder and Scully are called in to investigate Isaac's death, apparently he was beaten to death inside his market in a neighbourhood with a history of racial abuse. Police have ruled out racial abuse and they later retrieved a VCR surveillance tape showing the murder of one of the teenage killers of Luria, Tony Oliver. The murdered is unidentified but Mulder is very interested when Luria's fingerprints are found on Oliver's body.

Later, Jacob Weiss (Ariel Luria's father) shows the agents an anti-Semitic pamphlet left at his door and Mulder concludes that the person who made the pamphlets must have known who Isaac's killer was. They decide to interview Curt Brunjes who is the runner of a copy shop and when they show Brunjes photos of two teenagers suspected of the murder he claims he does not recognize them. Scully tells the shop owner that there are rumours going around that Isaac has risen from the dead so he can take revenge on his murder. Meanwhile one of the teenagers looks on in the interview via a security camera.

The two teenagers suspected of the murder, Banks and Macquire decide to dig up Isaac's coffin. While Macquire leaves Banks to get some tools, Banks pries the coffin lid open and finds Isaac's body inside but when Banks returns he finds Macquire's body buried in a mound of mud.

Mulder and Scully go to the crime scene and find a book under Isaac's body but when Mulder touches it it goes up in flames so they go to Kenneth Ungar who is a scholar. He tells the agents that it is a book on Jewish mysticism and he also notes a name that he finds on the book, Jacob Weiss. They later locate Weiss in an attic of a synagogue nearby Banks's hanged body dangling from a wooden beam. Weiss is taken into custody and confesses to the murders but Mulder is not so sure and thinks something unearthly caused the deaths.

Unger explains to Mulder after a mystical creature called the Golem which is believed to be made from the earth and that the word 'Emet' is inscribed on the back of it's hand. Unger tells Mulder that the only way to kill it is to erase the first letter 'E'.

Meanwhile, Brunjes is murdered by the Golem and when the agents examine the security video they find the culprit exactly matches the physical features of Isaac. Later Weiss is released from prison so he goes straight to the synagogue where he finds his daughter, Ariel Luria preparing for her wedding but when Weiss tries to stop her, he is attacked by the Golem. The agents discover Weiss and while Scully attends to his injuries, Mulder searches for Ariel but is attacked by the Golem. Ariel intercedes and continues with the wedding ceremony. The Golem places the ring on Ariel's finger and so Ariel wipes the 'E' off the creature's hand. The Golem crumbles into dust and is never seen again....