S4E8 · Tunguska

The episode opens in medias res to Dana Scully (Gillian Anderson) as she is brought before a Senate select committee to be questioned about the whereabouts of Fox Mulder (David Duchovny). Scully refuses to answer the committee's questions and attempts to read a statement denouncing the conspiracy within the government. Senator Sorenson threatens to hold Scully in contempt of Congress.

Ten days earlier, at Honolulu Airport, a courier returning from the Republic of Georgia (David Bloom) is searched by customs officers. One of the officers (Andy Thompson) removes a glass canister from the courier's briefcase and accidentally shatters it, exposing both men to the black oil. Meanwhile, in New York City, Mulder and Scully take part in an FBI raid against a domestic terrorist group. Mulder's tipster within the group is revealed to be Alex Krycek (Nicholas Lea), whom the terrorists released from the missile silo where he had been trapped. Krycek has turned against The Smoking Man (William B. Davis), and tells the distrustful agents that he can help expose him.

Krycek leads the agents to Dulles International Airport, where they try to apprehend a second courier carrying a diplomatic pouch from Russia. The courier leads the agents on a pursuit through the airport, but drops the pouch before escaping. The pouch is revealed to carry a seemingly unremarkable rock. Mulder has Krycek confined at the high rise apartment of Assistant Director Walter Skinner before having the rock analyzed at NASA 's Goddard Space Flight Center. Dr. Sacks, a NASA scientist, tells Mulder and Scully that the rock is a prehistoric meteorite fragment that might contain fossilized alien bacteria.

Skinner is approached by the Smoking Man, who demands that the pouch be returned. The courier breaks into Skinner's apartment and searches for the pouch, only to be thrown off Skinner's patio by Krycek. Meanwhile, Dr. Sacks cuts into the fragment, but inadvertently releases the black oil inside; the organism penetrates the scientist's hazmat suit and puts him in a coma -like state. Mulder travels to New York to visit Marita Covarrubias (Laurie Holden), who reveals that the fragment originated from the Russian province of Krasnoyarsk and provides the documents needed to travel there. Mulder reluctantly brings along Krycek, who is fluent in Russian.

In Charlottesville, Virginia, the Smoking Man is admonished by the Well-Manicured Man (John Neville) when the latter learns about Mulder's travels. Skinner and the agents are subpoenaed to appear before Senator Sorenson's panel over the missing pouch; when Skinner questions Scully about Mulder's whereabouts, she is not forthcoming. Meanwhile, as Mulder and Krycek hike through the forests of Krasnoyarsk, the former theorizes that the fragment may be tied to the Tunguska event, a mysterious cosmic impact that occurred in the area in 1908. The two men come across a slave labor camp, but are captured by the taskmasters and thrown into a gulag.

Skinner and Scully meet with Senator Sorenson, who questions them on the death of the courier and the location of Agent Mulder. Mulder talks with a fellow prisoner who tells him that innocent people have been captured and brought to the gulag to be subjected to experiments. Immediately afterwards guards burst into the room and inject Mulder with a syringe. When Mulder awakens he is in a large room bound with chicken wire along with many other prisoners. Black material is dumped onto his face, infecting him with the black oil.