THE RED AND THE BLACK

        You must be losing it, Mulder. I can beat you with one hand.

In the mountain wilderness of Canada, someone in a cabin writes a letter addressed to "Son" and expresses hopes that they may reconcile. The envelope is addressed to the FBI, and is given to a boy courier for mailing.

Fox Mulder (David Duchovny) arrives at the Ruskin Dam and finds a number of burned corpses, including those belonging to Quiet Willy and Dmitri. Dana Scully (Gillian Anderson) is found with only minor burns, one of approximately fifty survivors who were found nearby in the woods. Jeffrey Spender arrives looking for his mother, Cassandra (Veronica Cartwright), who is missing. Mulder meets with Scully about the incident, but she does not remember anything. Jeffrey sees Mulder and warns him not to get involved with his mother, who remains missing.

The Well-Manicured Man (John Neville) and other Syndicate Elders watch as their black oil vaccine is administered to Marita Covarrubias (Laurie Holden), which has yet to work. Later, The Well-Manicured Man meets with Alex Krycek (Nicholas Lea), who is being held captive aboard a Russian freighter. The Well-Manicured Man believes that the Russians possess a functional vaccine to the black oil, or else Krycek would not have infected the boy. With a working vaccine, resistance to the alien Colonists is possible.

A spacecraft crashes at Wiekamp Air Force base in West Virginia, and the surviving Rebel passenger is captured by the military. Mulder shows Scully more photos of the victims and, having found more implants in them, believes the implant in Scully may be able to answer all of their questions. The Syndicate meets over the capture of the Rebel. The Well-Manicured Man informs them of the existence of the Russian vaccine, believing that this makes resistance to the Colonists possible. If the vaccine is ineffective he proposes avoiding handing over the Rebel and instead forming an alliance with the Rebels, but the other Syndicate members believe this would be a suicidal course of action.

Under hypnosis, Scully recalls the Rebels burning her fellow abductees, as well as a Colonist spacecraft killing the Rebels and abducting Cassandra. During a meeting with Walter Skinner, Mulder continues to insist that the events have been orchestrated by the military and not by aliens. Meanwhile, the Russian vaccine seems to have no effect on Marita. The First Elder tells the Well-Manicured Man that they have already decided to turn the Rebel over to the Colonists. Jeffrey shows Scully a video of him talking about aliens while under hypnosis while he was a child, claiming his mother had forced him to make those statements.

Krycek is released and attacks Mulder in his apartment. He claims that a war is raging between the aliens and that the Rebel immolations are meant to halt the impending colonization of Earth. He also claims that the captured Rebel is critical to their plans and must not die. Scully visits Mulder and reveals she has been reconsidering her memories of abduction, while Mulder reveals he is newly taking them seriously as a result of his encounter with Krycek. Mulder and Scully head to Wiekamp Air Force Base, where the Alien Bounty Hunter—who is disguised as Quiet Willy—has come to kill the Rebel. However, Mulder witnesses a second Rebel arriving to seemingly kill the Bounty Hunter and rescue the captured Rebel. The Well-Manicured Man watches as the Russian vaccine is revealed to have been successful on Marita. Mulder is released by the military but is confused by what he saw. At FBI Headquarters, Spender receives the letter from Canada. In Canada we see the boy return the unopened letter to the cabin and the sender is revealed to be The Smoking Man

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