Dr. Jeff Eckerle, a renowned scientist, calls an exterminator to rid his basement of cockroaches. As the exterminator, Dr. Bugger, sets about his work in the basement of Eckerle's home, he suddenly grabs his throat, gasping for breath, and falls against a cement wall. Eckerle rushes to the basement, and looks on, horrified, as roaches swarm Dr. Bugger, engulfing his entire body.
     Shortly thereafter, Mulder strikes up a conversation with Sheriff Frass, who relays the news about the roach attack. Intrigued, Mulder inspects the exterminator's corpse, and phones Scully for her opinion regarding the bizarre incident. Scully suspects the man was probably allergic to cockroaches and died from anaphylactic shock. Shortly thereafter, the sheriff receives a report about a teenager who mutilated his own body with a razor after he became convinced that roaches were burrowing into his body. Scully again supplies a logical explanation, attributing the incident to a psychotic disorder caused by the victim's drug use. Mulder searches the drug den and turns up a cockroach exoskeleton, which he believes is made out of metal.
     Mulder takes the skin to a nearby hospital for examination. Meanwhile, hospital staff discover the dead body of Dr. Newton, who expired while using a toilet. An orderly describes how roaches completely covered Newton's corpse. Mulder again telephones Scully for advice. She attributes the death to an aneurysm caused by straining too forcefully.
     Sheriff Frass tells Mulder the federal government erected a facility in town to conduct experiments on cockroaches. Mulder sneaks onto the property, where he encounters Dr. Bambi Berenbaum, a voluptuous entomologist. Berenbaum, a federal agent with the USDA Agricultural Research Service, explains that cockroaches are being studied to determine the best method to eradicate them. She agrees with Scully's theory about an accidental importation of a new cockroach species-a species which is attracted to, rather than repelled by, the sight of human beings.
     Yet another body turns up at a nearby motel. Mulder finds one of the bugs trapped inside a roach motel, and brings it to Dr. Berenbaum for examination. The insect proves to be robotic, not organic. The discovery leads Mulder to Dr. Alexander Ivanov at the Massachusetts Institute of Robotics. He examines the robotic insect, but is stunned by its complexity. He suspects that, perhaps, the robot cockroaches were sent to explore Earth by an advanced alien race.
     When Scully arrives in town, she finds the community in a state of panic. She phones Mulder with a theory about Dr. Eckerle, who witnessed the exterminator's death. Eckerle is an alternative fuel researcher, who manufactures methane gas from manure. Scully believes the new species of bugs, which are dung-eaters, may have accidentally hitched a ride along with the manure samples.
     Mulder drives to Eckerle's lab, where the crazed doctor confronts the agent with a gun. Eckerle fires the weapon, missing Mulder but igniting methane gas. A huge explosion engulfs the research facility, killing Eckerle.