A TV news special report tells of law officers, chasing a stolen blue car near Elko, Nevada. From a camera in a helicopter, viewers watch as the car is stopped at a roadblock. The driver, Patrick Crump, is pulled from the car, struggling. An apparent hostage, his wife, is helped into the back seat of a highway patrol car, but a few seconds later the inside of the car is splattered with blood.
Mulder and Scully are in Idaho, on a "domestic terrorism" assignment, checking on large orders of fertilizer that could be used to make bombs. They see a TV news report about Crump, and decide to go to Navada, against orders from their new boss, Assistant Director Kersh. Scully inspects Vickie Crump's body at the morgue. It appears that her ear exploded. Another body has been found in a similar condition, and Scully concludes that the condition may be communicable. She orders full quarantine. Meanwhile, Crump has fallen ill in his jail cell with intense pain in his head. He is put in an ambulance; Mulder follows in his rented car. As the ambulance speeds up, Crump's pain eases. He takes a gun from an officer, stops the ambulance and takes Mulder hostage, ordering him to drive as fast as possible.
When Mulder slows his car for a traffic light, Crump goes into agony. Mulder begins to understand Crump's condition, and avoids an anticipated roadblock. Out of gas, Mulder tries to do a rapid fueling at a gas station, but the pump is turned off, so he and Crump steal another vehicle. He leaves a note behind in the car to tell Scully that the car must not be stopped. Crump thinks he and his wife are victims of a government experiment. In containment suits, Scully and other authorities visit the Crump residence -- a rural mobile home. The Crump's dog, outside on a leash, is agitated and as a blood sample is take from the dog, its ear explodes. Other dead animals are found, but a neighbor lady who is deaf is unharmed. There is some kind of government equipment near the Crump's property.
Entering California, a highway patrol officer on motorcycle hands Mulder a cell phone. Scully tells Mulder that she has learned that the Navy has part of an underground transmitting array for an ultra low frequency radio system running under the Crump property. They had a power surge that morning that disrupted television in four states. Scully theorizes that the surge created a condition in the inner ear that is somehow eased by speed along magnetic lines of force, or some such reason. She will fly ahead of Mulder and meet the car where the highway ends, inserting a needle into Crump's ear to relieve the pressure. Crump agrees, as his only way to survive. But when the car actually arrives, Crump's ear has already exploded and he is dead.
Mulder and Scully are in trouble with Kersh. Even though they may have saved lives to causing the Navy to shut down its low frequency array, they disobeyed FBI orders. Kersh informs them that they no longer investigate X-Files, and they'd better accept it. They go back to investigating "big piles of manure" in their domestic terrorism assignment.