As both Mulder and Scully try to find out a way of escaping from prison, a government conspiracy is in full flow. When Mulder escapes, he begins to find out what.

The prisoner next door to him tells him that he was exposed to something called the 'black cancer' which originated from the rock that fell in Tunguska in 1908. It seems that Mulder will die in here so he tells the prisoner that he can't be killed until he has killed Krycek. The prisoner therefore gives him his very own home-made knife which will allow Mulder to do this. But he is still trapped and is facing death.

Back in Washington, Scully and Pendrell investigate the organism that seems to have put the doctor in a coma state. They start to unravel the mystery when they discover a black organism living in the subject's brain. Meanwhile, back in Russia but this time in St.Petersburg, a retired KGB assassin named Vassily Peskow, is informed that the "cold war isn't over" so getting back to work, he travels to a horse farm belonging to the Well-Manicured Man in order to assassinate Dr. Bonita Chung-Sayre, a respected doctor on viruses in order to keep the truth from becoming known.

Later, Scully is due to testify before a Senate Sub Committee which prompts Skinner to ask Scully for more information about the diplomatic pouch and the rock it contained. Scully though is reluctant to answer. Skinner also brings it to the attention of Scully about the death of the doctor on viruses supposedly due to a 'riding accident' which surprises Scully because she happens to be an expert on Viriola viruses which is actually what Scully and Pendrell discovered.

Back in Tunguska, a long line of prisoners (including Mulder) are being taken to face another haunting experience involving the black fluid. Mulder spots Krycek laughing with one of the officials of the camp which prompts him to rush up to Krycek and knock him out. Waving his handy home-made knife around, Mulder manages to climb aboard a truck and smash through the gates of the camp. Unfortunately though the brakes on the truck don't work and Krycek (who happens to be aboard the truck) manages to fall off the back before the truck goes tumbling down an embankment with Mulder inside. Krycek manages to flee into the woods but is surrounded by a group of one-armed men who claim to be able to protect Krycek. Meanwhile, Mulder has managed to escape the wreckage and now hides underneath the leaves of the forest where his captures cannot find him.

Back to the present (shown in Tunguska), Scully is thrown in jail for not divulging the whereabouts of Mulder to the committee at the hearing. Explaining to Skinner, she says that they are purposefully avoiding the subject of the lethal toxin by covering it up with a pathetic story about where Agent Mulder is located. Later, in Tunguska, Mulder is discovered hiding by a harmless family who say that the only way Mulder can be saved is by his left arm to be amputated. Mulder though, wants to return to St. Petersburg. Meanwhile, while Krycek is sleeping, the group of men cut off his arm with a hot knife apparantely to 'save' him.

Later, Peskow suddenly arrives in Washington where he injects the doctor in a coma with a toxin which releases the worms from their host and kills him. Meanwhile, Scully is again being held in court for a second chance to confirm Mulder's whereabouts. Just as they are going to go down the same road, Mulder turns up much to the joy of Scully. This enables them to start talking about the extra-terrestrial toxin which soon brings the committee to disbelief. The court session is ajourned.

Mulder is determined to find the last bit of evidence of the lethal rock which they obtain by questioning one of Krycek's comrades who is currently being held in jail. He tells them that Krycek hid a part of the rock in Terma, North Dakota in a oil well. Peskow though is already two steps ahead of them and is in Terma where he has driven a truck full of explosives to the site of the well where he intends to ignite the oil to destroy the evidence. The agents arrive there by helicopter but they are too late and the well blows up. Mulder manages to save his life just in time. All the evidence is gone.

Back in St. Petersburg, Peskow opens his door to find Krycek there congratulating him on a good job. He is also seen with a prosthetic arm. Meanwhile, the agents have turned over their report on the case to the Committee which turns out to have been chaired by the Cancer Man who chucks the report in the garbage before anyone can read it.....