S5E20 · The End

In Vancouver, an international chess tournament is held at an arena between Anatole Klebanow, a Russian grandmaster, and Gibson Praise (Jeff Gulka), a young American prodigy. In the rafters, the Shooter, an assassin, prepares to fire at Gibson. However, Gibson senses the Shooter's presence and manages to discreetly dodge the shot, which kills Klebanow instead.

Elsewhere in Canada, the Smoking Man (William B. Davis) is found by Alex Krycek (Nicholas Lea). At FBI Headquarters, Walter Skinner (Mitch Pileggi) reveals to Fox Mulder (David Duchovny) that Jeffrey Spender (Chris Owens) is leading the case investigating the shooting. Despite Spender's request that Mulder not be involved, he bursts into the briefing and offers the explanation that the assassin was firing at Gibson, not Klebanow. Attending the meeting is Diana Fowley (Mimi Rogers), an acquaintance from Mulder's past. The Smoking Man is reunited with members of the Syndicate, including the First Elder and the Well-Manicured Man, who want him to help them with the situation concerning Gibson. Fowley accompanies Mulder and Dana Scully (Gillian Anderson) when they visit Gibson in Gaithersburg, Maryland. Mulder believes that Gibson can read minds, hence his expertise at chess. Scully learns that Mulder and Fowley know each other from long ago.

Mulder visits the Shooter, despite Spender's objections, offering immunity in exchange for testimony; the Shooter refuses. Gibson proves his abilities to a group of clinicians while Scully and Fowley watch. Meanwhile, a prison guard hands the Shooter a flattened Morley cigarette box, which conveys he's a dead man. Scully visits the Lone Gunmen, wanting them to analyze the data from Gibson. She asks them who Fowley is, and they tell her she worked closely with Mulder when he first discovered the X-files. The Smoking Man meets with Spender in the FBI parking lot but disappears when Mulder spots them talking.

Scully and Mulder present to Skinner on Gibson, who displays extraordinary brain activity. Mulder believes that Gibson can unlock all the mysteries in the X-Files and wants to make a deal with the Shooter. Skinner and Fowley think this may result in adverse attention from the Attorney General, and that the X-Files could be closed down if things go wrong. Mulder dismisses the risk.

Mulder meets with the Shooter again, who tells him that Gibson is a missing link. Mulder believes that Gibson has genes that are dormant in most humans. The Smoking Man dismisses the Well-Manicured Man's concerns about Mulder's actions. At the prison, the guard kills the Shooter. Fowley, protecting Gibson in a hotel room, is shot shortly afterwards, and Gibson is captured by the Men in Black. Skinner tells Mulder of the Shooter's death, and that a flattened Morley cigarette box was found in his cell. Mulder confronts Spender, accusing him of working with the Smoking Man.

The Smoking Man turns Gibson over to the Well-Manicured Man. Scully is informed by Skinner that the Justice Department is seeking to have the X-files shut down. Mulder realizes that this was all part of a plan. The Smoking Man takes Samantha Mulder 's X-file from Mulder's office, which he sets on fire. As he leaves, he meets Spender and tells him that he's his father. By the time Mulder and Scully arrive, the X-files are completely destroyed.