Inside a sports arena, two chess masters, a Russian man and an odd-looking 12-year-old boy named Gibson Praise, engage in a battle of the minds as an audience sits in reverential silence. High above the crowd, on a catwalk overhanging the arena, a sniper aims his rifle towards the back of the child's head. As the gunman slowly squeezes the trigger, the little boy announces "checkmate," and slides back in his chair. A gunshot rings out... and the Russian falls to the floor, dead. Meanwhile, two armed, masked figures close in on the cabin where the Cigarette-Smoking Man has holed up. A sensor alerts the Cigarette-Smoking Man to their presence, and he manages to kill one of them before making his escape into the woods. The second masked gunman gets the drop on his prey... and reveals himself as Alex Krycek.

Skinner briefs Mulder on the death of the Russian chess player. It turns out that the sniper is a former member of the National Security Agency. The case was assigned to Agent Spender, who specified that Mulder be excluded from the investigation. Despite this, Mulder and Skinner crash Spender's briefing. While viewing videotape of the assassination, Mulder reaches the conclusion that the shooter's target was Gibson--not the Russian--as the boy reacted in an almost precognitive fashion moments before the shot rang out. Spender disagrees with the theory. Agent Diana Fowley, an attractive woman in her thirties, opines that Mulder is correct. Spender rewinds the tape... and forms the same conclusion.

The Cigarette-Smoking Man meets with the Syndicate Elders. Labeling Gibson a threat, they ask for the Cigarette-Smoking Man's help in orchestrating his elimination.

Mulder, Scully and Diana Fowley visit Gibson inside a psychiatric hospital. The boy declines Mulder's invitation to match wits against a cheap chess computer... giving credence to Mulder's suspicion that the boy is not a chess master, but a mind reader. Tests on the child's brain reveal that Gibson is, indeed, clairvoyant. Later, Mulder visits the shooter in his cell. He offers him immunity from prosecution in exchange for his cooperation.

Scully cannot help but notice chemistry between Mulder and Fowley. She pays the Lone Gunman an unexpected visit. She gives them data from the tests performed on Gibson, and asks that it be analyzed. Scully also asks for information on Diana Fowley. The three men confirm that she and Mulder were an item back when Mulder graduated from the Academy and first discovered the existence of the X-Files. Scully returns to the psychiatric hospital intending to show Mulder the data she has accumulated. But when she approaches the observation room, she notices Mulder and Diana inside... and Diana holding Mulder's hand. Scully, a confusion of emotions, both personal and professional, leaves the hospital. When Mulder enters the hospital's parking garage to retrieve his car, he notices Spender talking to the Cigarette-Smoking Man. Mulder pushes Spender hard in the chest, demanding to know his business. Spender explains that he does not know the identity of the mysterious man. He then reveals that the shooter wishes to speak with Mulder.

Scully meets with Skinner and Mulder to reveal the results of the psychiatric tests on Gibson. It turns out that an area of the child's brain, dubbed the "God Module" by neurophysicists, exhibits extraordinary activity. Mulder believes the child's life is in danger because of his gift, as it might be the key to solving the unexplained phenomena contained within the X-Files. He also suspects that the assassin holds the key to the vast conspiracy working against him. Skinner points out that the very existence of the X-Files would be put at risk if he asks the Attorney General to grant immunity to the assassin. Later, Mulder approaches the shooter and asks him for information he can corroborate. He reveals that Gibson is a missing link--genetic proof of man's relationship to an alien race.

The Cigarette-Smoking Man puts his plan in motion. The assassin is murdered inside his cell. Shortly thereafter, a bullet strikes Fowley as she stands watch over Gibson. The Cigarette-Smoking Man delivers the child to the Well-Manicured Man and Krycek.

When Mulder sees Spender at the Bureau, he pushes him into a wall. He angrily accuses him of orchestrating Gibson's disappearance in conjunction with the Cigarette Smoking Man. Other agents restrain Mulder, dragging him away. Spender responds by stating that Mulder's days are numbered. Later, Scully informs her partner there is talk of shutting down the X-Files. That night, the Cigarette-Smoking Man sneaks into Mulder's office and steals a file on Samantha Mulder. He then addresses Spender face-to-face. He informs him that he is his father. Suddenly, a fire alarm sounds and agents make their way into the hallway. The Cigarette-Smoking Man disappears into the crowd. Later, Mulder inspects the damage to his office, where the cabinet containing the X-Files is a melted skeleton. Scully places her arms around her partner, offering support.