Skinner, Scully, Mulder and a dozen FBI agents participate in an undercover operation in a Washington, D.C. park. Its purpose: to catch Jacob Haley, a militia group member wanted on domestic terrorism charges. As Skinner and Scully monitor events from a surveillance van, Mulder and several other undercover agents slowly close in on their suspect, who meets with a Goateed Man sitting on a park bench. Haley hands the Goatee Man an envelope, then suddenly runs off. Mulder gives chase, unaware that the skin on Goatee Man's face and hands is slowly being eaten away. Scully jumps from the van, intending to warn her partner. But when she reaches Mulder, she is astounded to discover that the suspect eluded capture.
Scully voices her concerns to her partner, looking for some explanation as to why he allowed Haley to escape. But Mulder sidesteps the issue. Shortly thereafter, the agents attend a meeting of a counter-terrorism council, which is headed by Skinner and U.S. Attorney Leamus. During the meeting, Scully states that the Goatee Man was killed by some form of bioweapon. Skinner then shows those in attendance a photo of August Bremer, the militia group's mastermind. He notes that Bremer and Haley are reportedly vying for control.
Her curiosity piqued, Scully begins surveilling her partner's movements from afar. Mulder rents a room at a motel, where he has a heated telephone conversation with Haley, one that implies the pair are working together. Shortly thereafter, a BMW rolls into the motel parking lot, and Mulder climbs in. Scully tails the car, but her progress is halted when two sedans force her to stop. Four large men then approach her vehicle. Scully is escorted to a government building where, to her surprise, she is met by Skinner and Leamus. They explain that Mulder is participating in a deep cover assignment, the existence of which is known only to Skinner and Leamus. Someone in the militia group reached out to Mulder after he voiced his opinions about governmental conspiracies during a UFO conference.
The BMW transports Mulder to a remote farmhouse. There, Mulder is questioned by Haley, who accuses him of spying on the group. When Mulder fails to give acceptable answers, a Skin-Head Man pushes back on his finger, causing Mulder to scream in pain. The torture session continues until Mulder suggests a mole exists within the group. Suddenly, the Skin-Head man pulls back on the finger, snapping it like a piece of celery. When Mulder passes out, Haley turns to him and says, "I believe you." Meanwhile, Bremer tests the bioweapon on patrons at a small movie theater, killing fourteen people. But the question remains as to how the pathogen was spread to the victims.
When Mulder returns to his apartment, he is surprised by Scully. She tends to his broken finger and discusses the undercover operation. Unbeknownst to them, Bremer is secretly recording their conversation. Later, Mulder reports back to Skinner and Leamus. It is determined that the militia group intends to rob a bank. Mulder also relays word that Haley demanded copies of surveillance files of militia group members (hoping to flush out the mole). Leamus reveals he anticipated such a request, and already has redacted microfilm documents prepared. Mulder returns to the motel and gives Haley the microfilm. He is then transported back to the farmhouse, where the militia group is readying its assault on the bank.
Scully determines that the toxin was not developed by the Russians as previously believed. In private, she tells Skinner that the United States is operating a secret bioweapons program--and that someone in the government may have sent Mulder on a suicide mission. Later, it suddenly dawns on Scully that the source of pathogen's distribution is money.
Wearing monster masks, Mulder and the militia members storm a bank. Bremer accesses the vault and sprays the money with the pathogen. The group stages a successful getaway, and later Mulder realizes that the entire purpose of the break-in was to contaminate the money. Bremer pulls a gun on Mulder, announcing that his undercover work has been exposed. But Haley intercedes, noting that Bremer's alias was discovered on the microfilm, exposing him as the mole. Bremer responds by playing back the secret tape recording he made of Mulder and Scully's conversation. Bremer hands Haley a leather car key holder, allowing him to leave the group unharmed. But Bremer and the Skin-Head Man march Mulder away, intending to execute him. Suddenly, Bremer kills the Skin-Head Man. Bremer tells Mulder to run before they are both exposed. Mulder makes his way back to the bank, which has already been sealed off by Scully and Skinner. Scully explains that she recognized Mulder on a bank surveillance tape by the bandage on his finger. As the money is hauled out of the bank, Leamus tells the agents that the bills have tested clean. Scully accuses Leamus of having orchestrated the entire plan. Later, Haley slumps over in his car, his face eaten away by the biotoxin, which was transmitted by the key holder given him by Bremer.