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He is an FBI agent going on a hunt against his archenemy, the terrorist Castor Troy. This is because he killed his son (accidentally as he's aiming for Archer himself) while they're in a carnival. Archer lays an ambush to capture Castor and his brother Pollux at a small Los Angeles airport. During the ambush, Castor goads Archer with knowledge of a bomb located somewhere in the city, but is knocked into a coma before Archer can learn more.
Archer affirms the existence and size of the bomb from Pollux' documents, but Pollux refuses to talk to anyone but his brother. Archer's partner and friend Tito convinces him to undergo an experimental face transplant surgery by Dr. Walsh, replacing his face with Castor's. The procedure is kept a secret to only the three. Archer is incarcerated in the same high-security prison as Pollux, and slowly works on Pollux to learn the bomb's location.
Meanwhile, Castor wakes from his coma and discovers his face missing. With the help of his men, Castor forces Dr. Walsh to give him Archer's face, and then kills Walsh and Tito to prevent them from revealing the truth. Castor easily takes over Archer's life, including being with Archer's wife Eve and daughter Jamie. Castor goes to the prison to gloat to Archer, and then is able to arrange for Pollux' release under guise of sharing information, and then subsequently locates and disarms the bomb with much bravado. The FBI department is impressed with the new confidence Castor demonstrates as Archer.
Archer manages to escape from prison and finds his way to Castor's headquarters, and convinces Castor's men that he is Castor. He finds one of Castor's gang is a young mother named Sasha with her boy Adam who bears a strong resemblance to Michael. Archer takes sympathy on Sasha's attempt to lead a better life for Adam. Castor learns of Archer's escape and arranges a large FBI team to raid his headquarters. The raid is run in haste, causes a number of agents and Castor's men, including Pollux, to be killed. Archer, Sasha, Adam, and several others manage to escape. Back at FBI headquarters, Castor is lambasted by Archer's supervisor, Director Victor Lazarro, but Castor loses his patience and kills him; he is able to convince the rest of the department that Lazarro died by a heart attack, and he is promoted to Acting Director as funeral arrangements are made for Lazarro.
Archer finds Castor's promotion makes it impossible to approach him. Archer meets with Eve at the hospital where she works, and though not able to convince him of his identity, finds that she recognizes that her husband seems different. Eve obtains a blood sample from Castor and finds it does not match her husband's blood. When Archer returns, Eve is still confused but lets Archer know of the pending funeral which Castor will be present at. Archer persuades Castor's men to launch a non-lethal attack during the funeral.
At the funeral, Archer finds that Castor has anticipated his actions and has taken Eve hostage. Sasha is able to free Eve, but is fatally shot in taking a bullet for Archer, and Archer promises to watch after Adam for her. Castor attempts to take Jamie hostage, but she retaliates by stabbing him with a butterfly knife using a technique he taught her. Castor, with his identity blown, leads Archer on a speedboat chase. Archer forces Castor ashore, and attempts to subdue him through melee. Castor is cornered and attempts to cut open his face, making it impossible for Archer to get back, but Archer kills Castor with a spear gun. As the FBI surround the pair, Eve is able to convince the agents of Archer's true identity.
After Archer's transplant is discovered, the face transplant is reversed and now, Archer, back in his former self, returns home to his wife and daughter, and helps to introduce Adam into his new home.