Agts. Mulder and Scully traveled to a town in rural Indiana in response to a letter from a woman identified as Shaineh Berkowitz. In her letter, Ms. Berkowitz described two events, which she had experienced eighteen years apart. During both incidents she had become incapacitated, lost consciousness for three days, and awoke pregnant. The first experience had resulted in the birth of a son, identified as Izzy Berkowitz, now eighteen years of age. The second had occurred recently and was preceded, according to Ms. Berkowitz, by the sound of a song performed by the popular singer known as Cher, a smokiness in her room, and the entrance of a monstrous creature, having a "really gross face with big lumps all over his head." Ms. Berkowitz concluded her letter by noting that she had heard Agt. Mulder's name mentioned on an episode of the "Jerry Springer" television program.

At the Berkowitz residence, Agts. Mulder and Scully interviewed Ms. Berkowitz. They discussed the episode of the "Jerry Springer" program on which Agt. Mulder's name had been mentioned. Ms. Berkowitz stated that she was again pregnant despite having had a tubal ligation two years earlier. She further stated that her frying pan had been used during the recent intrusion and that the intruder, or possible intruders, had eaten a large quantity of peanut butter, and may also have consumed alcoholic beverages. Ms. Berkowitz described the intruder's monstrous face; Agt. Scully noted on the cover of a comic book in Izzy Berkowitz's bedroom a character fitting that description. Ms. Berkowitz identified the comic book character as The Great Mutato, which she stated was conceived and drawn by her son, Izzy Berkowitz. At that point Izzy Berkowitz arrived at the Berkowitz residence. When questioned by Agt. Scully why the suspect in his mother's case looked exactly like the character on the comic book he created, Izzy Berkowitz claimed to have witnessed the creature identified as The Great Mutato. He further claimed that numerous residents of the town had also seen the creature.

That night, Agts. Mulder and Scully, Izzy Berkowitz, a friend of Mr. Berkowitz identified only as Booger, and other friends of Mr. Berkowitz entered a nearby wooded area. Mr. Berkowitz placed a peanut butter sandwich on a tree stump, ostensibly as bait for The Great Mutato. Agts. Mulder and Scully discussed the impact of tabloid news and television talk shows on contemporary culture and the psychological bases of superstition and its relation to the current case. Subsequently, they heard a moaning sound coming from the nearby forest, identified by Mr. Berkowitz as that made by The Great Mutato. Observing a figure by the tree stump, the agents approached. The figure fled; the agents and others gave chase, but soon lost their suspect. In the woods they discovered an old man, later identified as Mr. Pollidori, who ordered them away from his property. The agents told Mr. Pollidori that they were looking for what was reported as a monster. He informed the agents that in order to find the "real" monster, they ought to visit his son, identified as Dr. Francis Pollidori.

Agts. Mulder and Scully interviewed Dr. Pollidori in his laboratory. Dr. Pollidori outlined his work with homeotic hox genes, describing that work as visionary and unprecedented. Showing the agents a film on the structural development of drosophila, Dr. Pollidori explained that his research and experiments had resulted in the alteration of a fly's physical structure; he then showed the agents an image of a fly with legs growing out if its mouth. Pressed by Agt. Mulder, Dr. Pollidori admitted the theoretical possibility of performing similar experiments on human beings. After Dr. Pollidori left the lab, en route to what he described as an international conference in Inglestadt, Germany, Agt. Scully insisted that experimental mutations would be virtually impossible to reproduce in human beings, and if they were possible, no scientist would dare perform them on humans. Agt. Mulder countered that the power to cause such mutation might indicate a strong desire to cause it in human beings.

Later, at his residence, Dr. Pollidori packed for his trip and discussed with his wife, identified as Elizabeth Pollidori, his desire not to have children. Mrs. Pollidori appeared distraught. After Dr. Pollidori drove away, leaving Mrs. Pollidori alone, the residence was draped in exterminators' tenting, of the sort used during termite fogging.

The next morning, at J.J.'s Country Diner, Agt. Mulder was treated to a show of extraordinary friendliness by townspeople, apparently hoping Jerry Springer would be inspired by the agents' investigation to visit the town. In the diner, Agt. Mulder observed an unidentified female reporter taking notes. Agt. Scully, entering the diner, showed Agt. Mulder an issue of the local paper in which was reported verbatim their private discussion of the night before regarding tabloid news, folklore, and superstition.

The agents proceeded to the Berkowitz residence, where they accused Izzy Berkowitz of having recorded their conversation as part of a publicity hoax in order to promote his comic book creation. Mr. Berkowitz produced a tape recorder containing a tape of the agents' conversation. Rewinding further, the agents also heard a fuzzy recording by the singer known as Cher of a song entitled "The Sun Ain't Gonna Shine Anymore," which Ms. Berkowitz identified as having heard during the intrusion resulting in her recent pregnancy. On the tape, the agents also heard a moaning, which Agt. Mulder identified as the same voice they had heard the previous night. Meanwhile, at Dr. Pollidori's residence, an unidentified figure danced in a cloud of gaseous white smoke to the same song.

Agts. Mulder and Scully removed the tape from the Berkowitz residence. Agt. Mulder suggested they send the tape to Bureau Headquarters to have the voice on the tape separated from the rest of the sounds and analyzed. Alluding to the classic novel Frankenstein, he also implied that Dr. Pollidori ought to be considered a suspect in the case.

Driving past the Pollidori residence, Agt. Mulder noted the presence of a termite tent draping the home, and reminded Agt. Scully that Ms. Berkowitz's letter had referred to the presence of a gaseous cloud during the event resulting in her recent pregnancy. The agents left their vehicle and approached the Pollidori residence on foot, hearing the song, "Gypsys, Tramps, and Thieves", recorded by Cher, coming from inside the house. They entered the residence, weapons drawn, and discovered the presence of a white gas. In the upstairs bedroom, the agents discovered Mrs. Pollidori, lying in her bed in a state of unconsciousness. Both agents were then overcome by the gas and lost consciousness. The old man identified as Mr. Pollidori, wearing a gas mask, observed the unconscious agents.

Later, Agts. Mulder and Scully were discovered on the bedroom floor by Dr. Pollidori and a state trooper. Mrs. Pollidori, now conscious, described having witnessed the presence of a creature which matched the description given by Ms. Berkowitz. Agts. Mulder and Scully expressed skepticism. Agt. Mulder stated that Mrs. Pollidori might have been impregnated. Agt. Scully suggested that the events were part of a publicity hoax. Nearby, the unidentified female reporter took notes. Agt. Mulder noted the presence in a frying pan of an unusual residue similar to that described by Ms. Berkowitz. He also located an empty jar of peanut butter in a trash receptacle.

In the cellar of Mr. Pollidori's farmhouse, the creature identified as Mutato watched the film "Mask." He was then given a peanut butter sandwich and addressed as "son" by Mr. Pollidori. Mr. Pollidori then left the cellar and entered his farmhouse. While he was looking at photographs in an album, he was surprised by a visit from Dr. Pollidori. Dr. Pollidori physically attacked Mr. Pollidori and strangled him to death.

The next morning, Mutato discovered Mr. Pollidori's body and, appearing overcome with grief, buried the body in the barn. Meanwhile, Agt. Mulder entered J.J.'s Country Diner, where he was treated with disapproval and scorn by customers and staff. He observed the headline of the local paper, which reported the agents' suspicion that events at the Berkowitz and Pollidori residences were part of a hoax. Noting the agitation of people on the street outside, Agt. Mulder and others left the diner and proceeded to the post office, where a postal worker was announcing to an angry mob that Izzy Berkowitz, also present, had perpetrated the hoax. The postal worker had intercepted a package addressed to Mr. Berkowitz which contained masks that resembled Mutato.

Agt. Scully, arriving at the scene, informed Agt. Mulder that the residue found in the Pollidori frying pan was an agricultural product used to anesthetize herds of animals, and that Mr. Pollidori was registered with the FDA as possessing the product. The agents proceeded to Mr. Pollidori's farmhouse and entered the barn, where they discovered the anesthetic, as well as the site of Mr. Pollidori's burial. They also discovered the unidentified female reporter, hiding in the hayloft, who informed them that she had observed the creature burying Mr. Pollidori's body. In the farmhouse, the agents reviewed the photos of the creature as a child in Mr. Pollidori's albums. An angry mob of townspeople led by Dr. Pollidori then arrived at the farm. Dr. Pollidori announced that he had seen the "monster" and urged the mob to search for it. As the mob left to search the barn, Agt. Scully noted to Agt. Mulder that if Dr. Pollidori had seen the creature, then he too had been present at the farm. Noting the presence of a figure at the cellar door of the farmhouse, the agents entered the cellar.

In the cellar, the agents discovered much memorabilia related to the singer known as Cher. They then discovered Mutato and urged him to surrender. Agt. Mulder reminded Agt. Scully that if the agents failed to remove Mutato, the mob would murder him. The mob, meanwhile, accidentally set the barn on fire. People and livestock began fleeing the barn. As Agts. Mulder and Scully and Mutato attempted to exit the cellar, the unidentified female reporter observed them and alerted the mob, forcing the trio to retreat back into the cellar. The mob entered the cellar and surrounded Agts. Mulder and Scully and Mutato. Dr. Pollidori claimed that Mutato had murdered his creator, Mr. Pollidori. Mutato, over the objections of Dr. Pollidori, explained to the mob that he had actually been created by Dr. Pollidori, and rescued and cared for by Mr. Pollidori, who had attempted to emulate Dr. Pollidori's experiments to create a mate for Mutato. Those experiments failed. Mutato pleaded with Dr. Pollidori to create a mate for him and offered to take blame for the murder of Mr. Pollidori. Dr. Pollidori alleged that he was unable to recreate Mutato. The mob appeared to grow sympathetic to Mutato, who submitted to arrest. Dr. Pollidori was also taken into custody.

As the arrest took place, Agts. Mulder and Scully again discussed the novel Frankenstein. Agt. Scully reminded Agt. Mulder that unlike the creature in the novel, Mutato would find no bride. Cryptically, Agt. Mulder demanded to speak to someone he identified as the writer. Shortly thereafter, in a caravan of vehicles, Agts. Mulder and Scully, Mutato, and many of the townspeople drove to a performance given by the singer known as Cher, who performed the song "Walking in Memphis."

Shortly after they delivered their babies, who strongly resembled Mutato, Ms. Berkowitz and Mrs. Pollidori appeared on the "Jerry Springer" television program.