FBI Special Agent Sean Archer (John Travolta) survives an assassination attempt by freelance

domestic terrorist and homicidal sociopath Castor Troy (Nicolas Cage), but the bullet pierces through
Sean's chest and strikes his son Michael, killing the boy.

Six years later, Sean's vendetta against Castor culminates in his team's ambush of Castor and his
younger brother/accomplice Pollux (Alessandro Nivola) at Los Angeles International Airport. Castor
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.

Sean affirms the threat is real, but is unable to convince Pollux to reveal where the bomb is located. At
suggestion of his partner Tito Biondi (Robert Wisdom) and Special Ops specialist Dr. Hollis Miller (CCH
Pounder), Sean secretly undergoes a highly experimental face transplant procedure by Dr. Malcolm
Walsh (Colm Feore) to take on Castor's face and appearance. Sean is taken to the same high-security
prison where Pollux is, and slowly convinces Pollux that he is Castor, gaining information on the bomb's
location. Meanwhile, Castor wakes up from his coma prematurely and discovers his face missing. He
calls his gang, and they force Dr. Walsh to put Sean's face on him.

Castor visits the prison and surprises Sean. He taunts his nemesis with how he burned down Dr.
Walsh's lab with Walsh, Tito and Miller inside to eliminate all evidence of their switch and will take over
Sean's life. He leaves Sean to languish while he convinces Pollux to "reveal" the bomb's location in
exchange for release from prison. Disarming his bomb in a dramatic fashion, Castor-as-Sean gains
respect from Sean's fellow FBI colleagues. Castor gets close to Sean's family that Sean neglected over
his vendetta: he romances his wife Eve (Joan Allen) and saves his daughter Jamie (Dominique Swain)
from an attempted rapist.

Sean escapes after staging a riot, and retreats to Castor's headquarters. There, Sean meets Sasha
(Gina Gershon), the sister of Castor's primary drug kingpin, and her son Adam who reminds Sean of
Michael. Sean learns that Adam is Castor's son, whom he once had planned to put under foster care.
Castor learns of Sean's escape and hastily assembles a team to raid his headquarters. The raid quickly
turns into a bloodbath, killing numerous FBI agents and several members of Castor's gang, including
Pollux; Sean, Sasha, and Adam are able to escape. Sean's supervisor, Director Victor Lazarro (Harve
Presnell) blames Castor for the numerous slayings. Castor, furious over Pollux's death, kills Victor and
makes it look like a heart attack. Castor-as-Sean is promoted to Acting Director as plans are made for
Lazarro's funeral.

Sean finds safety for Sasha and Adam and approaches Eve. He persuades her to take a sample of
Castor's blood and his own to compare their blood types at the hospital where she works to prove he is
Sean. Convinced of her husband's identity, she tells him that Castor will be vulnerable at Lazarro's
funeral. At the ceremony, Sean finds that Castor has anticipated his actions and takes Eve hostage.
Sasha arrives, and a gunfight ensues; Sasha manages to save Eve after taking a bullet. Before she
dies, Sean promises to take care of Adam for her and not allow him to grow up with a life of crime.

Castor flees the church with Sean pursuing him. After killing two federal agents, Castor briefly takes
Jamie hostage, but she escapes by stabbing him with a butterfly knife Castor ironically gave her earlier
for self-defense. A speedboat chase ensues wherein Sean forces Castor to shore by collision, then
bests Castor in a melee fight. Castor mutilates his/Sean's face to taunt him but Sean kills Castor with a
spear gun. FBI agents arrive and address Sean by name, having been convinced by Eve of Sean's true
identity. After the face transplant surgery is undone, Sean returns home, with Adam having been
adopted into his family to keep his promise to Sasha.