In Tunguska, Mulder has survived his ordeal for now, but is still being held captive in a Siberian Gulag. The prisoner in the next cell explains that all the men in the camp are injected with "black cancer" until the toxin finally kills them. Escape is impossible. Resistance is futile. Mulder swears he will survive, long enough at least to kill Krycek. Impressed by Mulder's will to survive, the prisoner gives Mulder his own home-made knife. Back in Washington, Dr. Sacks is alive after being infected by the black worms from the rock that was recovered in the diplomatic pouch, although he is comatose. For Scully and Agent Pendrell, the medical mystery starts to unravel when tests reveal a black vermiform organism attached to his brain's pineal gland.

St. Petersburg. A former KGB assassin, Vassily Peskow, comes out of retirement when a messenger from "Comrade Arntzen" requests his help, and tells him the Cold War isn't over. Peskow makes his way to a horse farm which belongs to the Well-Manicured Man where he assassinates Dr. Bonita Chung-Sayre, a well-known authority on viruses and the Well-Manicured Man's personal physician.

Due to testify before the Senate Subcommittee hearing, Skinner presses a reluctant Scully for more information about the pouch and its contents. Skinner surprises her with his news: the pouch's intended recipient was the late Dr. Chung-Sayre, who was killed in a "riding accident."

Tunguska. The prisoners, including Mulder, are on the march. Nearby, Krycek is laughing it up with Mulder's tormentors. The sight spurs Mulder to action. Armed only with the knife, Mulder steals a battered truck and makes his escape, knocking Krycek into the back of the truck and taking him along for the ride. The chase ends when the truck's brakes give out. Krycek bails out before the crash, but Mulder is trapped inside. Krycek flees through the woods where he runs into a group of men - all of which are missing their left arm. Krycek tells them he is an escaped prisoner, and the men take him in. Meanwhile, Mulder has survived the accident and hides in the forest from his pursuing captors.

In Washington, Scully is jailed for contempt of Congress when she refuses to reveal Mulder's whereabouts at the Senate hearing. As she explains to Skinner, someone with a secret agenda is deliberately obfuscating the case: focusing on a missing FBI agent, rather than the existence of a toxic biohazard of extra-terrestrial origin and the deaths of those connected to it.

Mulder is discovered hiding in the woods by a family, who explains that the villagers' only means of saving themselves from the fatal experiments is a drastic one: amputation of the left arm. Mulder must persuade them to take him to St. Petersburg, or they may amputate his arm to "save" him. Unfortunately for Krycek, his rescuers "save" him as he sleeps.

Peskow continues his mission, paying a visit to the comatose Dr. Sacks whom he injects with the same amber fluid that had been shot into Mulder at the Gulag. The worms emerge, and he kills Sacks. At the Senate hearing, Scully is just about to be charged with contempt again...when Mulder appears, arm intact. Mulder's presence puts the attention back on the rock and the biotoxin, but when Scully tries to bring up the subject of the biotoxin's extraterrestrial origin, her claims are not taken seriously. Mulder interrupts the hearing, challenging the skepticism of the Senators when the most conservative scientists and science journals have every reason to believe that life exists outside our terrestrial sphere. Taken aback by Mulder's statement, the chairman of the subcommittee abruptly adjourns the hearing, calling for a recess until the evidence can be properly evaluated.

Following the lead that Dr. Chung-Sayre was the supervising physician at a nursing home in Boca Raton, Mulder and Scully travel to Florida to investigate. She and Mulder arrive too late. Peskow has already poisoned all of the patients and black worms have emerged from their deceased bodies. Mulder realizes a similar experiment to the one being conducted in Russia had been conducted at this nursing home. Still bent on finding a trace of evidence left behind, Mulder and Scully travel to New York where they interview the head of the militia group Krycek was running with. The militia member tells them Krycek told them his name was Arntzen, and that Krycek approached them. Everything Krycek told him was a lie. They also learn that the US government covered up their knowledge that Soviet-developed "black cancer" was deployed by Saddam during the Gulf War. Mulder now believes the whole thing was a set up from the beginning by someone who doesn't want the rocks in American hands. Finally, he discovers where Krycek is hiding another rock: Terma, North Dakota, in the stolen truck carrying the Militia's fertilizer bomb.

Again, Peskow is one step ahead of Mulder and Scully. He drives the truck to a Canadian oil refinery, intending to destroy the remaining rock. Mulder and Scully arrive too late to prevent Peskow from igniting a fiery explosion which engulfs the last piece of evidence. Both barely escape with their lives.

The final report on their investigation is turned over to the Senate subcommitte, but in vain. The Cigarette-Smoking Man controls the Senator who chairs the committee. In St. Petersburg, Peskow returns home to find Krycek, sporting a prosthetic left arm, who commends Peskow for a job well done.