In Kazakhstan, former Soviet Union, two teenage boys watch as a UFO disappears behind a mountain top. The boys run off to tell their families, but as they sprint through the woods, they come upon an area filled with burning automobiles. A screaming man, his body ablaze, appears out of the dense smoke, causing the boys to run. One of them, Dmitri, takes refuge in the woods. The next morning, he is discovered by Krycek, who is in the company of a unit of Russian soldiers. With the boy in custody, Krycek and his men approach Maria Covarrubias, who, along with U.N. troops, is sifting through the burned out wreckage. Krycek tells Maria he knows who she works for--and to tell her superiors he has a witness (Dmitri).

     Back in the United States, Mulder takes part in a visiting lecturers forum. He disagrees with the opinions voiced by his fellow panelists regarding a woman referred to as "Patient X," an apparent abductee who seeks answers as to why aliens are on Earth. Mulder maintains that there is no complicity between the military and alien abductions. Instead, he believes the government is developing biological warfare and hiding the fact by concocting stories about "little green men." When the discussion ends, Mulder is approached by Dr. Werber, the man who performed regression hypnosis on him five years earlier (leading Mulder to believe his sister was abducted). Werber reveals that he is Patient X's doctor. He arranges a meeting between Mulder and the woman, Cassandra, believing that she will change his mind regarding his new theory. Cassandra believes the aliens are on Earth to deliver a message. But something, she fears, has gone wrong.

     Krycek extracts information from Dmitri by subjecting him to a beating. He then orders a Russian doctor to expose the teenager to the alien black oil. The liquid enters Dmitri's body through his mouth and nose. Dmitri, his eyes and mouth sewn shut, is then transported back to the US on a Russian freighter. Meanwhile, Covarrubias briefs Syndicate members on the mysterious burn site in Kazakhstan. Covarrubias believes the act was aimed at the Syndicate, and reveals that Krycek captured a witness at the site. Krycek phones the group and offers to trade Dmitri for all research information pertaining to a vaccine against the black oil.

     At the FBI building, Scully is approached by Agent Spender, who identifies himself as Cassandra's son. Spender tells Scully that his mother is a very disturbed woman. Later, Scully tells Mulder about the conversation. She then peruses Cassandra's medical file, growing intrigued when she realizes Cassandra claims to have been abducted at Skyland Mountain, the same site where Scully was taken by Duane Barry. The file also reveals that Cassandra has an implant in the base of her neck. Mulder brushes off the findings, agreeing with Spender's conclusion. But so intrigued is Scully by the developments that she pays Cassandra a visit at the psychiatric hospital. There, she grows unnerved when Cassandra tells her that some nights she awakens feeling as though she must be somewhere, but not knowing where to go.

     Meanwhile, a group of abductees gather at Skyland Mountain. As an Unknown Man drives down the mountain road, he encounters faceless men chasing another man. One of the faceless men drives a metallic wand into the Running Man's back, setting him ablaze. Later, Mulder and Scully inspect the site. The situation forces Scully in the opposite position she would normally take, for despite a lack of evidence, she believes the event is linked to her abduction. The agents are contacted by Cassandra, who warns "they" must be stopped. The agents are then approached by Spender, who explains that his mother was part of a UFO cult.

     Back at the Syndicate office, group members conclude that the latest burning is aimed at sabotaging their work. Quiet Willy is dispatched to deal with the situation. Meanwhile, Covarrubias rendezvous with Krycek at the freighter, which is docked in New York Harbor. The two share a hungry kiss, then exit so they can be alone. When Krycek returns, Dmitri has vanished. The Well-Manicured Man appears, demanding to know where the boy has gone.

     After examining the evidence, Mulder concludes the victims of the mass burning were led to Skyland Mountain by the government when it triggered the implant devices. But he is at a loss to explain why they were killed. Their conversation is interrupted by a call from Covarrubias, who informs Mulder of the similar incident in former Soviet Union, and of the witness, Dmitri. Suddenly, the black oil oozes from Dmitri, and Covarrubias drops the phone.

     Scully suffers an attack--not unlike the one Cassandra described earlier. She travels to Ruskin Dam, where a throng of people have gathered, including Cassandra, in the company of Quiet Willy, and Dmitri, the stitches having been torn from his eyes and mouth. A glowing ship passes overhead and disappears over adjacent treetops. Suddenly, screams are heard from the far edge of the congregation, where faceless men wielding alien weapons set people ablaze.