On September 9, 1991, FBI Special Agent Sean Archer survives an assassination attempt by freelance terrorist and homicidal sociopath Castor Troy, but the bullet penetrates Archer's chest and strikes his son Michael, killing the boy. Six years later, Archer's vendetta against Troy culminates in his team's ambush of Troy and his younger brother and accomplice Pollux at the Los Angeles International Airport. Troy goads Archer with knowledge of a bomb located somewhere in the city set to go off in a few days, but he is knocked into a coma before Archer can learn more.
Pollux, in custody, affirms the bomb is real, but does not know its location. At the suggestion of his partner Tito Biondi and Special Ops specialist Dr. Hollis Miller, Archer secretly undergoes a highly experimental face transplant procedure by Dr. Malcolm Walsh to take on Troy's face, voice, and appearance. Archer is taken to the same high-security prison where Pollux is being held, and slowly convinces Pollux that he is Troy, gaining information on the bomb's location.
Meanwhile, Troy unexpectedly awakens from his coma and discovers his face missing. He calls his gang, and they force Dr. Walsh to transplant Archer's face onto him. Troy then kills Dr. Walsh, Biondi, and Miller, the only three that knew of the transplant.
At the prison, Archer prepares to tell Biondi of the location but is surprised when Troy appears instead, with Archer's face. Troy goads Archer that no one knows of the transplant, and that he will take over Archer's life. Pollux is freed when he willingly tells Troy-as-Archer of the bomb's location, and Troy disarms the bomb in a dramatic fashion. Troy-as-Archer earns admiration from the FBI office, while Troy becomes close to Archer's wife Eve and daughter Jamie, whom Archer had been neglecting while chasing down Troy.
