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Robert "Bobby" Torrence, a prisoner incarcerated at the Cumberland State Correctional Facility in Virginia, receives a mysterious package containing a pig's leg. Shortly after his exposure to the appendage, Bobby suffers several goiter-like protrusions on his face and neck. He is relocated to the prison infirmary, where two physicians, Auerbach and Osborne, attend to his lesions. Bobby's cell is later cleaned by two other convicts, Paul and Steve, who realize that the laundry cart offers them an opportunity for escape.
The FBI assigns Mulder and Scully to aid in the capture of the escapees. However, the agents remain mystified as to why the Bureau is interested in the case. Scully's suspicions are aroused when Dr. Osborne claims he was sent to the facility by the Centers for Disease Control. He explains that a mysterious flu-like illness has taken the lives of ten prisoners, and that the escaped convicts may be carriers of the disease. Scully realizes that the bodies of the dead prisoners are marked for incineration. Osborne catches Scully sneaking about the cadavers. As Scully watches, horrified, a pustule on a cadaver suddenly bursts, spraying Osborne with a white fluid.
Meanwhile, Paul and Steve murder a man and steal his motor home. At a gas station, Paul places a call to his girlfriend, Elizabeth, informing her of his freedom. Angelo, a gas station attendant, finds Steve doubled-over in pain inside a restroom. Paul knocks Angelo unconscious with a tire iron, and he and Steve escape. Mulder and members of the U.S. Marshal's office find Angelo's unconscious body at the station. Mulder traces the last phone call made at the gas station's pay phone to Elizabeth's residence.
The convicts make their way to Elizabeth's home. Steve's condition worsens. Without warning, a pustule on Steve's skin bursts open, spraying Elizabeth with puss. Mulder and the marshals storm Elizabeth's home, but they arrive too late. Steve is already dead, and Paul is not to be found.
Scully traces the package mailed to Bobby Torrence to a company called Pinck Pharmaceutical. While examining Bobby's corpse, she pulls the hard slender carapace of a dead insect from an open boil. Osborne, who is near death, tells Scully that he works not for the CDC, but for Pinck Pharmaceutical. He explains how the company regularly finances the exploration of rain forests for potential drug application. A field entomologist sent the lab samples of an insect, Faciphaga Emasculata, which is parasitic in nature and attacks the human immune syndrome. Now the company-and the government-are trying to cover-up the fact that prisoners were used as guinea pigs for Pinck Pharmaceutical's experiments. Aided by information supplied by Elizabeth, Mulder tracks Paul to a bus station. Realizing that Paul is the only remaining person who can testify against the government and Pinck Pharmaceutical, Mulder attempts to take him alive. A sniper's bullet rings out, and Paul is killed.