In a flashback, FBI Special Agent Sean Archer (John Travolta) is taking his six year old son Michael for a ride on the Griffith Park carousel in downtown Los Angeles. As they ride around, Archer runs his hand over Michael's face and smiles.
Meanwhile, Castor Troy (Nicolas Cage) sets up a suppressed sniper rifle on the hill overlooking the carousel. He takes aim at Archer, waits until he gets a clean shot, and fires. The bullet hits Archer in the back, and he and his son fall off the horse, leaving a noticeable bloodstain on the horse's mane. Three balloons are seen drifting away into the sky.
Moments later, Archer is shown lying on his stomach, in pain, the bullet having gone cleanly through his body as bystanders rush over to him. Though bleeding, he sees Michael lying a few feet away, dead, the bullet having struck him in the head. Tears stinging his eyes, Archer crawls over and holds his dead son's body while Castor looks up from the scope of his rifle, stunned to see that he has just killed a child. The carousel horse Archer was riding on spins round and round and quickly fades out.
Six Years Later:
Archer is the field agent in charge of the FBI's Los Angeles field office and has been relentlessly pursuing Castor ever since the assassination attempt. Castor is a career terrorist, responsible for countless terrorist bombings, aircraft hijackings, and political assassinations, among other crimes. Archer looks at a wall documenting a long list of commendations given to him for his years of dedicated hard work and service, then somberly holsters his pistol and approaches his coworkers. We see that Archer carries the burden of his son's death on his shoulders at all times from his walk. He is agitated that his closest agents, Tito Blondi (Robert Wisdom), Wanda (Margaret Cho), Buzz (James Denton), and Loomis (Matt Ross) have no information on Castor's latest whereabouts.
Meanwhile, Castor poses as a minister to sneak into the Los Angeles Convention Center, where he assembles and arms a big bomb called "Sinclaire". As he leaves, he cannot resist the opportunity to headbang to a choir singing the Hallelujah chorus and grope a blonde choir girl.
At the FBI office, Archer finishes up a heated phone call with director Victor Lazarro (Harve Presnell). His secretary Kim Brewster (Romy Windsor) comes in to inform him that his wife Eve is on line 1 trying to call him. But simultaneously, Tito bursts in to tell Archer that Castor's brother Pollux just chartered a jet at a local airfield and paid it in cash. Archer immediately orders Tito to get an undercover agent planted on the plane. Tito is about to protest that they don't have any sign of Castor, but Archer counters Pollux "doesn't fly without big brother!" and marches out of the office, ignoring the fact that his wife is on hold.
Pollux Troy (Alessandro Nivola) is shown waiting impatiently in his convertible on the tarmac of a local airfield with his cronies Leo (Tommy Flanagan) and Lars (Dana Smith). He is relieved when Castor drives up in his own car. He climbs out and walks over to Pollux, and converses as Leo and Lars change his coat and sunglasses. Pollux is annoyed that Castor is running 26 minutes behind schedule. Castor lights a cigarette and asks Pollux if he hasn't deviated from their plans. Pollux admits that he paid for the jet himself to save them time. Castor reminds him that that is for the boys to handle so they can hide their movements, but he's not going to kill Pollux for such a screw-up because he loves him too much to do such a thing. He then bends over and quickly ties Pollux's shoelaces. Castor then tempts Leo and Lars with a gold money clip of $100 bills, only to snatch them away. He and Pollux then break into grins as he advises his men to stay away from downtown on the 18th, when things are going to be a little.... "smoggy". Castor and Pollux then board the plane, where they are greeted by Winters, an undercover agent posing as a flight attendant, whom Castor quickly seduces.
As the plane turns and prepares to start its takeoff roll, the pilot suddenly sees a Humvee on the runway, driving towards them. Simultaneously, Pollux looks out the window just as multiple police cars and a helicopter suddenly appear behind the jet and give chase. Castor gets up from his seat and rushes into the cockpit to take a look at the oncoming vehicle. Not to his surprise, Archer is driving the car, and Tito is riding shotgun.
At that point, Winters whips out her pistol and trains it on Castor. Pollux promptly throws his briefcase at her, holds her down, and beats her senseless. Castor puts a pistol to the pilot's head and orders him to fly the plane. The plane and Archer continue to close in on each other. It looks as if Archer is on a collision course with the landing gear, but he swerves at the last second and drives past the plane, then swings a U-turn to fall in line behind the plane. Archer then floors on the gas pedal. He has pulled up alongside the wings when the cabin door suddenly opens and Castor pushes the disarmed Winters out the door, and makes Archer watch him execute her with a bullet to the back. Archer stops the Humvee and promptly jumps into the helicopter, and takes off before Tito can protest.
Seeing Archer closing in, Castor puts his pistol to the pilot's head and orders him to take off. Archer promptly lowers the helicopter and rams the skids against the left wing flaps, jamming them. The pilot makes several futile attempts to pull back on the throttles, until the flaps break off completely. Trying to see what is keeping his plane on the ground, Castor peeks out the wing exit door. He raises his pistol and fires at Archer. Several bullets pierce the glass, but Archer ducks down, unharmed. Castor ducks back inside, while Archer sticks his pistol out and shoots out the left engines. Sparks issue from the engines and the engine fire alarm goes off on the pilot's control panels. Castor promptly executes the pilot, takes his seat at the controls, and quickly diverts the plane off the runway, putting it on a collision course with a hangar. Castor powers down the throttles, just seconds before the nose of the plane smashes through the glass windows in the side of the hangar and sends debris and parts flying everywhere.
Archer lands the helicopter as the other police units screech to a halt around the back of the plane and officers begin taking up positions. Sparks fly as Castor whips out twin pistols, jumps out of the plane, and opens fire. One agent standing on the wing of the plane is shot dead instantly, as is a cop standing on the ground. Pollux draws a submachine gun, fires a volley at Archer, and jumps out, following Castor. Archer jumps onto the roof of a police car and fires his pistol. Tito fires a submachine gun, driving Pollux further back into the hangar. Castor then breaks cover and fires both pistols rapidly. In the exchange, Loomis is hit, a bullet shearing off part of his left ear.
Castor calls out to Pollux, but Archer shoots at a water hose pipe. The bullet bursts a joint in the pipe, spraying water into Pollux's face. Pollux is driven out from cover, at which point Tito grabs him from behind and shoves him into a wooden shipping crate. Wanda then kicks him in the chest, then throws him on his stomach and handcuffs him. Meanwhile, Castor ambushes and shoots a SWAT officer at point-blank range with his pistol, then uses the officer's shotgun to shoot another agent. He then turns to see Tito and Wanda handcuffing Pollux, who cries out to Castor. Castor ignores him and rushes deeper into the hangar. A few agents haul Pollux away while Archer and a group of agents and cops rush in and split up to search for him.
Deeper in the hangar, Castor hides and lies in wait. Archer enters, his pistol drawn, searching between the stacks of shipping crates. He turns his weapon when he hears the echo of Castor reloading his pistol. Archer breaks cover and finds another agent, Berkeley, in the line of fire. He shouts a warning to Berkeley, but it comes too late. Castor turns and fires, hitting Berkeley in the back and killing him instantly. Archer fires once at Castor. Castor fires his shotgun at Archer, sending Archer scrambling for cover. Castor then drops the shotgun and draws his second pistol. Another agent, Buzz (Jamie Denton), draws his pistol and breaks cover. Archer tackles him to the ground just as Castor turns on Buzz and opens fire. Archer raises his pistol and his backup revolver and fires back at Castor. They continue firing until both run out of ammunition.
Archer takes cover behind a wooden shipping crate and reloads his pistol. Simultaneously, Castor reloads his pistols. Hearing the sound of clicking, he looks up to see Castor standing above him. Archer scrambles behind some crates as Castor opens fire on him again. Archer shoots a hook tying a steel pulley chain to the ground, grabs the chain, and uses it to take the high ground as he fires at Castor. Castor slides down a ramp, firing and shooting a submachine gun-wielding agent. He lands next to an active turbine.
Before Castor can stand up, Archer lands next to him and jams his pistol to his neck. Castor laughs and dares Archer to shoot him because he only has one round left in his weapon. They stand up and train pistols on each other. Engaged in a Mexican standoff, Castor tries to convince Archer to turn against his fellow men and try terrorism-for-hire, though it is clear he's trying to provoke Archer. Castor takes the opportunity to brag that he has a bomb that will deliver "Hell"-A the biblical plague it deserves, though Archer believes he is bluffing. Castor also brags that he knows Archer will just drive his family crazy now that his enemy will be locked up.
Asking if Archer's daughter Jamie is "ripe", Castor tries to shoot Archer, but the magazine clicks empty. He gets on his knees and breaks down, seemingly scared, but it is actually an act as we see that he is using the opportunity to secretly grab a knife from his pocket. Then he breaks into a grin and dares Archer to pull the trigger, singing, "I'm ready! Ready for the big ride, baby!" He promptly stands up, knife in his right hand. Archer kicks Castor's hand, disarming him. He then kicks Castor into the backdraft of the turbine. Archer hits a button and the turbine produces a sudden blast of hot air that sends Castor flying backwards until he hits a ventilation grate and falls motionless.
Archer returns home, and we see that his family life is less than optimal. His daughter Jamie gets in trouble a lot, and his relationship with his wife Eve seems somewhat distant due to all of the time he's spent looking for Castor. Nonetheless, he assures Eve that he will petition his boss to grant him a desk job so he can spend time rebuilding their relationship.
Back at the office, the employees congratulate Archer as he slowly walks into the office, looking crestfallen. His secretary gives him a bottle of champagne that has been sent by the CIA to commend Archer for stopping Castor. Archer tries to refuse it, unhappy with the fact that it says "Just for you" and does not have the names of all the agents shot dead in the shootout.
Archer logs onto his computer and presses some buttons to declare the Castor Troy case closed. He is interrupted when Tito and a Special Ops agent, Hollis Miller (C.C.H Pounder), come in. Miller produces a floppy disk found in Pollux's briefcase. Archer plugs it into his computer. Graphics of an animated woman come up to the tune of suggestive music, as well as the sound of audible moaning. The words "My name is Sinclaire, and I am going to blow you AWAY!" show up on the screen. As "AWAY!" shows up, the animated woman briefly flashes into a skeleton. Schematics of "Sinclaire" show up on the screen. Archer identifies it as a biological weapon. Miller warns that the fall out would be enough to flatten much of LA, and Archer realizes Castor was not bluffing about a biblical plague.
Getting more information on the bomb, though, is more difficult because Pollux will only talk about the bomb with Castor, and Castor is presumably deceased. An attempt to interrogate Pollux about the bomb schematics fails due to Pollux fooling the polygraph, and Archer refuses to take Lazarro's suggestion that he just let the matter go. Miller tells Archer that they could put an undercover agent in a prison cell with Pollux to get him to slip information, but Archer shoots that down. Miller proposes that there might be an alternate solution.
Miller takes Archer out to the Walsh Institute, a private medical institution that specializes in various types of state-of-the-art surgical operations. Archer enters the recovery ward, where, to his disbelief, he sees that Castor is in a medically induced coma and is on life support. Miller assures Archer that Castor is not going anywhere, demonstrating this by stubbing out her cigarette on Castor's skin, to which Castor does not even twitch. Miller, and the institute's director Dr. Malcolm Walsh (Colm Feore), give Archer an ambitious proposal: they would like Archer to take Castor's face and voice, then go into Erewhon Prison posing as Castor to extract information on "Sinclaire" from Pollux.
Dr. Walsh reveals that he is capable of performing surgeries to alter the facial appearance or voice of a person. To demonstrate, he and Miller show Archer into the observation deck for another operating room where surgeons are working on Loomis, the agent shot in the ear during the shootout with Castor in the hanger. As Dr. Walsh continues talking, lasers are shown constructing a new earlobe, that is then surgically stitched onto the stump of Loomis's original ear. Dr. Walsh explains that the surgery they propose Archer undertake to become Castor is much less permanent than what Loomis is getting. He explains the more technical details: Archer's blood type does not match Castor's but this will not be something Pollux will notice, and the height difference is easy to correct. Archer's skin and eye pigment color is also close enough to Castor's to be a reasonable match. Laser shears will be used to trim Archer's hair to Castor's length and appearance, microplugs to build up additional chest hair, an abdominoplasty that rebuilds Archer's midsection to more closely resemble Castor's. Dr. Walsh then shows Archer the true innovation: a morphogenetic template, the inside of which is modeled on Archer's skull but has an exterior modeled to resemble Castor's face, meaning he won't feel any different at all.
Archer finds the whole plan insane and starts to leave, but Miller stops him, reminding him that he has chased Castor for many years. He is convinced that getting Castor's gang to talk is easier, even though Miller warns him that Castor will effectively win if the bomb blows up.
Archer decides to instead first try interrogating known associates of Castor's. On the first two guys he tries to interrogate, he grills them so intensely that one of them pees in his pants. Late at night, he interrogates Castor's longtime girlfriend Sasha Hassler (Gina Gershon). She refuses to talk at first, but Archer warns her that she is on probation for previous criminal charges including harboring Castor, and gets her to talk by threatening to put her son Adam up in a foster home. She finally claims that she hasn't seen Castor in years. Archer then interrogates Sasha's brother Dietrich (Nick Cassavetes), who functions as Castor's bomb and weapons supplier. Archer tells him that the bomb has his signature written all over it. Dietrich scoffs, stating Archer has no real evidence against him. Things go sour when Dietrich decides to insult Archer by asking him about his deceased son. Archer snaps with rage, tackles Dietrich to the floor, and jams the barrel of his pistol into Dietrich's eye. Dietrich finally admits that all he knows is that the bomb goes off on the 18th.
As he watches Sasha and Dietrich leave the office, Archer is met again by Tito and Miller. Archer does not want to submit to the operation without Lazarro being notified, but Miller tells him that this is actually a black bag operation, meaning that it is classified and off-the-books (no paperwork), and Archer is not allowed to tell Lazarro or Eve anything about the mission. Feeling that he has nothing to lose, Archer accepts the mission.
After giving farewells to Eve and Jamie, Archer heads to the Walsh Institute and prepares for the surgery. He gives Tito his wedding ring and tells him to hold onto it for safekeeping. He asks Dr. Walsh if he can also restore the scar from the bullet wound Archer received from Castor years ago after the operation is over. Dr. Walsh agrees. Archer leaves Tito and follows Dr. Walsh to prepare for sedation.
The surgery begins. Archer and Castor are both sedated, then are wheeled into the operating room on separate tables. Dr. Walsh first uses a pen to trace the area of skin to be removed from Archer's face. He then uses a special laser to run along the line and isolate the skin. A suction cup is then lowered, and pulls off the entire section of skin comprising Archer's forehead, eyelids, nose, mouth, cheeks, and chin, exposing the raw muscles. Dr. Walsh then deposits the original skin on a facial template stored in a container of water to keep it from drying out. The same process is then repeated on Castor while a technician cuts Archer's hair. Castor's face is then put on top of Archer's exposed muscles and then connected to the rest of his skin muscles. Then the blood vessels are reconnected and the surgery is completed.
A few days later, Castor is back in his own hospital bed, his head wrapped up in bandages like a mummy. Meanwhile, Archer (now played by Nicolas Cage) wakes up and his bandages are unwrapped. He freaks out upon seeing Castor's face in the mirror and tries to destroy it with the base of a coat hanger. He is quickly calmed down by Miller and Tito, who administer a sedative. Archer calms down, and he asks Tito and Miller to burn his new face once he's gotten the information he needs.
Archer then notices that his voice hasn't changed yet. This problem is fixed with the next part of the operation. Dr. Walsh implants a microchip in Archer's larynx, and warns him to be careful as something as mundane as a sharp blow or violent sneeze could dislodge it. Dr. Walsh then plays back a short clip from an audiotape of Castor talking normally (in which he states "Peach. I could eat a peach for hours"), and instructs Archer to repeat back the line. It takes a few tries, but eventually Archer is able to get his voice to perfectly emulate Castor's. Archer is reminded that he has six days until the bomb goes off to get information from Pollux.
Meanwhile, at the LA Convention Center, the bomb's clock continues counting down.
Archer is next seen being led by Tito up to the helicopter landing pad where guards from the Erehwon Prison ("Nowhere" spelled in reverse) are waiting to pick him up. Tito tells him he has two days to get Pollux to talk, after which Miller will come in to withdraw him regardless. Archer is still complaining about an itch as he adjusts to his new face. Tito helps him by massaging his cheeks with his thumbs. Two prison guards grab Archer and begin leading him to the helicopter. He gives a longing look towards Buzz, Wanda, Loomis and Tito as they see him off. A blindfold is then lowered over Archer's face.
When Archer's face is unmasked again, he is shirtless and under a bright spotlight in a dimly lit room, being watched over by several guards. The prison warden, Walton (John Carroll Lynch), comes in, shines a flashlight in Archer's face, and analyzes him, telling him, "You are now the property of Erewhon Prison. A citizen of nowhere. The Geneva Convention is void here; Amnesty International doesn't know we exist. When I say your ass belongs to me, I mean exactly that." Archer's feet are then clamped tight in magnetic boots tied to a field that allows the guards to monitor the location of every prisoner 24/7.
Archer is then shown in the cafeteria line, trudging along as a nature channel plays images of various landscapes 24/7 on a large TV monitor. All of the inmates stop what they are doing upon seeing Archer. Archer comes dangerously close to blowing his own cover when he's stopped by another inmate that he recognizes as Burke Hicks, whom he arrested many years ago for stalking the UN Secretary General, a crime for which Hicks has always claimed he was framed. Archer is turning around and about to talk to Pollux when another inmate, a hulky Russian named Ivan Dubov, who seeks revenge on the real Castor ever since Castor had three-way sex with his wife and sister, attacks him. Dubov gives Archer an intense beating, throwing him around, leaving Archer with a bloody nose. After a brief moment to catch his breath, Archer regains his composure, and eventually gets the upper hand, defeating Dubov with a lunch tray. He's shocked at how close he's come to becoming the very likeness of his enemy. At the end of the fight, Archer's magnetic boots are clamped to the EM field and Walton prods him in the back with a stun gun. He then warns Dubov of the consequences he will face the next time he picks a fight with someone.
Back at the Walsh Institute, the real Castor is still asleep. His heart rate begins accelerating, and then he suddenly bolts upright. He is stunned to find that his face is completely wrapped in bandages. He pulls them off and discovers that the skin on his face is gone, leaving the muscle exposed. He touches the exposed muscles to verify that he is not hallucinating. Despite being in great pain, he hobbles over to the edge of the room and sees Archer's old face floating in a jar. He calls Lars and Leo on a phone in his wing and tells them to come immediately.
Lars and Leo abduct Dr. Walsh and transport him to the Institute in their car. They march him to the operating room at gunpoint, where they find Castor sitting in a chair, smoking a cigarette and watching the videotape of the surgery while listening to classical music (the video itself was recorded so Dr. Walsh could undo the surgery after the mission was completed). Watching the tape finish, Castor starts clapping, finding the entire thing very impressive. Castor advances towards Dr. Walsh, who, frightened, asks Castor what he wants. Castor claps his hands several times and we see his faceless face appear reflected in Dr. Walsh's glasses to reply, "Take one goddamn guess."
Back at Erehwon, Archer sits down with Pollux and successfully manages to extract information from him about the bomb. Later, he is in his cell when a guard stops by to tell him that he has a visitor. Archer is escorted to the visitor's room. Once he is in the room, the magnetic boots are activated, securing Archer's feet to the floor. He is hoping the visitor is Miller and Tito coming to release him. Instead, to his shock, in walks Castor Troy (now played by John Travolta), wearing Archer's old face and business suit, and all too happy to see that Archer is locked up in prison under his name. He likens the effect as being like looking into a mirror, only not. He is mildly annoyed about having his face cut off to disturb his coma and thrusts a newspaper article into Archer's face about a recent fire that destroyed the Walsh Institute and killed Dr. Walsh and two of his lab technicians.
Hearing the news from Castor, images flash through Archer's head of Dr. Walsh, Miller and Tito tied up and gagged on the floor of the Institute as Leo and Lars douse them with jugs of gasoline. One of them then flicks a Zippo lighter and drops it in a puddle of gasoline, starting a fire that burns them alive.
Castor then flashes Archer's wedding ring into Archer's face, as he casually reveals that he has killed Tito, and has destroyed any evidence that Archer could potentially use to prove who he is. Now he has plans to abuse Archer's job and even make love to Eve. Archer does not take this well and immediately tries to strangle Castor with his bare hands, but is stopped when guards rush in and restrain him. Castor thanks Walton for saving him, then departs while Archer can only resign himself to his new predicament.
Upon returning to the city, Castor immediately heads for his new house. As he is driving through the neighborhood, he looks in utter disbelief at all of the nicely manicured lawns and well-kept houses. He is distracted enough that he "accidentally" overshoots his own house right in front of Eve as she is walking to her car. He backs up to the curb, and smirks as his climbs out of the car. Eve chides Castor for finally forgetting where they lived. Castor insists that she give him a break, as every house looks the same. Eve asks Castor about his "vital assignment". Castor spaces out for a moment, but finally realizes that this refers to Archer's current impersonation of him, and gives a lie about an "out-of-body experience" (which in a way is partially true). He can't help but stare at her butt as she leaves for work at the hospital.
Castor goes inside and sits down at a desk in the living room, to settle himself down in his new life. He quickly finds Eve's diary in a drawer. He is somewhat stunned, upon reading a recent entry, to find that Archer hasn't had sex with Eve in over two months. Before he can dwell on the matter, he is distracted upon hearing his favorite song "Papa's Got a Brand New Bag" playing from Jamie's bedroom. He heads upstairs to find Jamie talking on the phone with her boyfriend while smoking a cigarette in just her underwear and a cropped t-shirt. Castor quips, "Hmm, the plot thickens...." Jamie, angered at Castor's invasion of her privacy, tries to slam the door on him, but Castor forces his way in, itching for her hidden stash of cigarettes. He narrowly comes close to blowing his cover by calling her "Janie" until he notices her name stitched on her bed pillow and corrects himself. Jamie is confused why her "father" has taken up smoking, to which Castor explains, "You'll be seeing a lot of changes around here. Papa's got a brand new bag." He then slowly backs out of the room while singing along to the music.
At Erehwon, Archer tries to come to terms with the reality that Castor has taken over his life. If anything could make him feel worse, it is when he learns that Castor has cut a "deal" with Pollux to turn state's evidence that also includes immediate release from jail.
Pollux is taken to the FBI office, where Castor plays "good cop" by treating him to a gourmet meal. Castor comes into the observation room, where Wanda and Buzz offer him their condolences for Tito's death. Castor shrugs them off. There is a brief disturbance when Lazarro comes in and confronts Castor to point out that cutting a deal with a lowlife like Pollux is something the real Archer would never do. Castor dismisses him, claiming that he's trying "fresh tactics". After everyone else leaves the observation room, Castor switches off the videotape, then enters the interrogation room and turns off the microphone while reminding Pollux that he's supposed to be snitching. Pollux tells Castor that seeing Archer's face on him makes him want to cough up his tiramisu. Castor proposes that they can do better if Pollux just "confesses" to the location of the bomb, thinking he will look a lot more impressive and gain media attention that Archer will envy if he single-handedly disarms the bomb.
Armed with Castor's "tip" from Pollux, the police converge on the Convention Center and hurriedly evacuate the building. Inside, Castor watches over two bomb squad technicians trying to disarm the bomb. There is one minute and 15 seconds remaining on the clock. The techs tell Castor that the codes are protected by a tamper switch that will take them several hours to bypass. Castor sternly orders them to leave. Once they are gone, he goes about disarming the bomb in dramatic flair. He bypasses the protective systems, then punches in the disarm code to deactivate the bomb with just two seconds remaining on the clock. Satisfied, he then closes the timer panel.
After watching Castor being interviewed on CNN, Archer is shown sulking in his cell, clearly a broken man. At the FBI office, meanwhile, Castor revels in the glory as the other agents congratulate him for disarming the bomb. In contrast to Archer, who is known for usually darkening the mood of his victories by reminding his men of the agents killed in their gunfights, Castor is all smiles, wears his sunglasses indoors, and thanks his men for putting up with him for all the years he was an insufferable bore. Some of the agents, like Archer's partner Wanda, wonder if Castor just had surgery (which seems to strike a small chord with Castor). He is also more tender and affectionate with Eve than the real Archer is. For instance, when Castor is told by his secretary that the president and his wife are both on the phone trying to contact him, Castor asks her to put the president on hold.
Desperate, Archer realizes that the only way he can stop Castor is to break out of prison, so he asks Burke Hicks about the odds of escape during exercise hour. Hicks tells him he can't escape: he can only get his boots off if he is taken down to the clinic to get shock treatment. Archer immediately notices a guard pulling out a pack of cigarettes and knowing that Castor smokes, he gets an idea. He breaks out of line, walks over to the guard, and demands a cigarette. When the guard orders him to get back in line, Archer punches him, instigating a fight with several other guards, who grab him and drag him away even as he yells to the incited inmates for someone to give him a match.
Down in the clinic, Dubov is getting shock therapy in the chair, having apparently picked another fight and failed to heed Walton's warning following his earlier fight with Archer. When they are done with Dubov, they pull him out of the chair and Archer, being dragged by his shoulders, is put in the chair. He successfully manages to get Walton to light a cigarette for him. As they are securing him, Archer tells Dubov that he didn't touch Dubov's wife or sister and knows that they are waiting for him.
The guards are about to put the arm restraints on Archer when Dubov suddenly clubs Walton over the back. Several guards hear the raucous and charge Dubov with batons. Dubov swiftly disarms each one of them, and Archer breaks free of the chair. A guard on the catwalk above opens fire with a submachine gun. Archer grabs a pistol and shoots him. Archer then takes cover as another guard appears and opens fire, forcing him into a corner. Dubov takes cover behind a stretcher. The guard fires at Dubov until Archer suddenly shoots him in the foot from below, and he collapses. The elevator doors open on the clinic floor and several guards appear. They open fire on Dubov and continue shooting until he shoves the gurney into them, disarming them.
Seeing two more guards coming on the catwalk, Archer grabs a bottle of sulfuric acid from the medical supply cabinet and chucks it upwards. Archer then shoots the bottle in midair, causing a small explosion that knocks one guard off the catwalk and forces the other one to retreat. Archer and Dubov then jump up to the catwalk and start running. The other guard stands up, but Dubov takes the first guard's submachine gun and shoots him. Archer then climbs up a ladder, scales a wall, and jumps on another guard, tackling him, as a riot breaks out in the exercise hall.
In the control room, panic breaks out as Dubov suddenly fires his submachine gun through the door. One guard fires at Archer as he runs along another catwalk, and continues firing until Dubov shoots him from behind. He then begins killing the guards in the control room until Archer arrives and orders him to stop. Archer tells the two remaining guards to leave, then sits down at the computer and starts typing in codes hoping to overload the security system. Before he can start, another guard opens fire on them, sending Archer diving for cover. Dubov fires his submachine gun and offs the guard and one other guard, and continues shooting until a third guard, who had taken cover, stabs him in the leg with a knife.
Archer then frantically types codes in to disable the security system, as Dubov whips and overpowers the guard who stabbed him, then tosses him over the railing into the cafeteria. Sparks fly as Archer overloads the TV screen. Just then, a bloodied Walton appears on the cafeteria floor, raises a rifle at Dubov, and fires. Three bullets hit Dubov in his chest. Dubov flails around and falls over the edge. Archer grabs him by the barrel of his gun and tries to pull Dubov back up. However, Dubov is weakened by his wounds. His grip slips and he falls to his death. Walton fires up at Archer, but is stopped when Burke Hicks and a couple other inmates surround him and apparently beat him to death.
Now safe, Archer makes his way up a stairway to the roof, only to find that the prison is an offshore oil platform in the Pacific Ocean just off the California shore. Before he can think about how he is out of luck, a helicopter appears. Archer runs and jumps off the edge of the helicopter platform as the gunner opens fire on him. Archer lands on the next deck down, and runs for the edge, only for the helicopter to show up and chase him back across the deck. He lands behind some oil cans. One shot causes a spark that lights Archer's feet on fire. Archer quickly removes his socks and does a running jump off the platform into the ocean. Archer does not surface and the helicopter pilots presume him deceased.
Back at Castor's house, it is Michael's birthday. Castor is roped by Eve into going to Michael's grave. Castor watches Eve place some toys on the angel-shaped tombstone. She breaks down crying in Castor's arms. Castor appears to be ashamed of himself for his own actions. When Castor returns to his office later that day, he is told by his coworkers that Archer has escaped from prison. Suspicious, he asks to see the body. When he's told it has not been recovered, Castor realizes that Archer is alive and will be coming for him.
After his jailbreak, Archer swims to shore. That night, still in his prison shirt, he steals a car from a valet parking lot, then drives over to the hospital where Eve works. He makes a call from the car phone and tries to warn Eve about Castor. However, his vocal chip causes him to speak with Castor's natural husky voice, which Eve does not recognize, instead of his real and much more nasally voice. She thinks someone is impersonating her husband and she hangs up on him. Frantic to alert someone he trusts to Castor's whereabouts, Archer calls the FBI office and asks to be put through to Lazarro, hoping to warn him, but to his dismay, he is transferred by the operator to Castor. Hearing Castor pick up the phone, Archer quickly hangs up and continues driving, switching off a radio report about the police manhunt Castor has declared on him. He then has to lower his head and make a quick right turn when he spots a police car approaching in front of him.
Unable to alert any of his colleagues or his wife, Archer decides to drive to the penthouse apartment where Dietrich lives. In the apartment, Dietrich is in the middle of a phone call as he enters his apartment and is stunned, then delighted upon seeing Archer-as-Castor. He invites Archer in and takes him upstairs to the second floor of the apartment, where several of Castor's old buddies and their girlfriends are hanging out. They all are pleased to see "Castor".
Archer sits down in a chair and Dietrich hands him a box containing some of Castor's regular contraband: several joints, prescription pills, a box of Chiclets, a money clip, and two gold-plated pistols (identical to the ones Castor was utilizing during the earlier shootout with Archer when they both had their original faces). He takes a moment to pick up the pistols to see how they feel and forces himself to take drug-laced water.
Dietrich asks Archer what he plans to do. Archer declares that he's going to use their help to take down Castor. Castor's other accomplices point out that "Archer" is a supercop, leading Archer to disclose details about himself, like the fact that his own house security code is the same as Michael's birthday. To explain how he knows so much about himself, Archer explains that "he" sleeps with Castor's wife. As to what he plans to do once he abducts Castor, Archer claims he wants to take Castor's face....off and stick it on himself. Naturally, Castor's pals think Archer is just spouting pure gibberish.
Feeling his body rejecting the drugs, Archer dismisses himself from the conversation and rushes to the bathroom. He tries to rinse his face clean, then he looks in the mirror and immediately draws one of his pistols on the reflection. Archer quickly talks himself out of his panic attack, and is interrupted by the arrival of Sasha. She glowers at him as he turns around, a slasher-style grin frozen on his face. He insists that he is not dead, at which point Sasha slaps him.
Meanwhile, Castor is in his living room and in the middle of a heated phone call with Pollux. He reminds Pollux that once he is able to use Archer's job to get rid of their criminal rivals, he'll be set and get his old face back. He is interrupted by music, walks over to the window and sees Jamie's boyfriend Karl (Danny Masterson) pulling up in the driveway with Jamie in tow. As Jamie prepares to get out of the car, Karl attempts to advance on her. She turns him down, however Karl gets more insistent and more forceful in his advances. Seeing the struggle, Castor quickly hangs up the phone on Pollux. Karl has forced himself onto Jamie and is holding her down when Castor suddenly smashes the window with his foot, pulls him out of the car, and then gives him a vicious beating, before slamming his head against the roof and ordering him to apologize. After extracting an apology, Castor throws him aside one last time for good measure.
Minutes later, Castor is talking to Jamie about the incident. As they talk, Castor begins to see past the exterior Jamie has put put in front of her family and sees what really is bothering her inside (something the real Archer has failed to notice): she has never come to terms with Michael's death at Castor's hands, has outwardly blamed Archer for not doing a better job in protecting their family and has mistrusted him since. As consolation, and not wanting to see Jamie get hurt, he gives her a butterfly knife for "protection", and instructs her to, if she gets attacked, stab the would-be attacker in the thigh and twist the blade so that the wound won't be able to close.
Back at Dietrich's penthouse, Archer is shirtless and lying facedown on a bed, with Sasha sitting next to him. He is woken up when Sasha nibbles his shoulder, and mistakenly addresses her as Eve. Realizing she's not Eve, he bolts awake and instinctively grabs one of his pistols. Sasha takes off Archer's pants and tries to make advances on him. Archer naturally freaks out. Unbeknownst to either of them, Pollux is standing on a roof across the street watching them through binoculars. Amused to see that Archer is beginning to "enjoy" being his enemy, he phones Castor.
Archer is finally able to get Sasha off him and puts on a leather jacket. She tells him to leave, recalling threats Archer made with his original face to put her son Adam up in a foster home. Upon seeing Adam, Archer is surprised to learn that Castor is Adam's biological father, something the real Castor has never had knowledge of. He immediately begins to regret threatening her, realizing that Sasha is just a single mother struggling to raise Adam to avoid a criminal life.
Meanwhile, alerted to Archer's whereabouts, Castor sends an FBI SWAT team to take up positions on the rooftop across the street and train submachine guns at the windows of the penthouse.
Inside, Archer learns that Adam is five years old, almost the same age his own son Michael was when he died, and also learns that Sasha has kept the fact that Adam is Castor's son a secret, fearing someone would hurt Adam to get to Castor. Sasha encourages Adam to meet his "father". Archer puts his hand on Adam's face and immediately has a flashback, recalling running his hand over Michael's face on a carousel ride just before his death. Seeing so much of Michael in Adam, Archer accidentally blurts his real son's name while hugging Adam, to Sasha's confusion. Sasha quickly grabs Adam and pulls him away from Archer, asking Archer what is wrong with him.
On cue, an FBI agent across the street fires a grenade launcher. A smoke grenade suddenly crashes through the bedroom window. Archer quickly pulls Sasha and Adam to the ground as the SWAT team opens fire with submachine guns, raking the windows with bullets. The men and women gathered in the loft immediately panic. Dietrich, Aldo and the other thugs quickly grab their weapons.
While taking cover behind the bed, Archer quickly grabs Adam's headset, muffling the shots so that he hears "Somewhere Over the Rainbow" playing instead. While this happens, an officer can be heard on megaphone ordering the inhabitants to surrender.
In the living room, a SWAT officer smashes one of the skylights and rappels in, firing a submachine gun. Just before his feet hit the ground, Dietrich raises a shotgun and shoots him. As another agent fires a submachine gun from the roof, Archer grabs Adam and he and Sasha rush into the other room. Another SWAT officer rappels through the side window. One thug covers Archer, Adam and Sasha and fires his pistol to drive the officer back. Some other SWATs burst in through the front doors, but this thug dives to the ground and fires a submachine pistol, forcing them to retreat.
Meanwhile, Dietrich uses his shotgun to shoot another SWAT officer on the second floor, sending the officer crashing through the railing. The officer lands on the lower level, dead, just feet from where Archer and Sasha have taken cover. Archer is shocked to see one of his own colleagues die in front of him. Sasha grabs the officer's submachine gun and she and Archer start to run. As several more of Castor's men burst in, Archer aims a pistol and yells at them to hold their fire. Surprisingly, the officers comply. Archer and Sasha then dive for cover as the officers fire on Dietrich. Dietrich picks them off with individual shotgun rounds. The other thugs then shoot at the officers in a vicious exchange of gunfire. An officer then rappels through a window near Archer. Archer kicks him back through the window, then when the officer swings back into the apartment, hits him across his visor, knocking him out.
Dietrich then yells to Archer to hand him Adam. As Sasha exchanges submachine gun fire with a SWAT officer, Archer hands Adam over to Dietrich, who takes him to the bedroom. The officer Sasha was shooting at is eventually hit several times and falls dead. She then rushes one of the other women up the stairs to safety. Another officer starts to pursue them, but Archer raises a pistol and shoots him in the knee, knocking him down.
As Adam rides the shootout out, we see a timelapse montage pass as the thugs and the SWAT officers exchange fire and "Somewhere Over the Rainbow" drowns out shouting and gunfire. Officers and thugs alike are both shot dead in the furious gun battle.
The montage ends when Archer grabs Adam from his hiding place just as an officer opens fire on him. Archer hands Adam over to Sasha, who rushes downstairs to the lobby. As she enters the lobby, Archer's partner Buzz, wearing a balaclava, corners them with a pistol. She promptly kicks him and disarms him. Buzz climbs to his feet and prepares to fire on Sasha, when Archer suddenly collars him, puts a pistol to his head and orders him to drop his weapon. Instinctively, Buzz complies. Archer then spins him around, pulls off his balaclava, and is stunned to recognize him. Before he can explain anything to Buzz, he hears Dietrich approaching. Buzz tries to grab Archer's pistol, but Archer swiftly disarms him and knocks him unconscious, then shoots the ground next to him just as Dietrich, who has just shot a few more SWAT officers, arrives.
Just then, they hear footsteps. Archer has his pistol drawn and sees Castor stealthily walking down a flight of steps. Castor raises his pistol and aims it at Archer. Detecting Sasha moving, he aims his gun in her direction. When he draws a bead on her, Dietrich notices and quickly moves in the way just as Castor fires. The bullet hits Dietrich in the side of his neck. Clutching the wound with his right hand, he tells Sasha to run and exchanges a quick kiss on the cheek before she goes. Archer arrives, but it's too late to save Dietrich. Dietrich thanks Archer for the good times they had before he collapses and bleeds to death.
Archer grabs Dietrich's submachine gun and heads into the front lobby. He gets a glimpse of Castor running through a back pathway. Archer raises his submachine gun and fires a burst at Castor, shattering several mirrors. There is a moment of silence, then in a mirror, Archer spots Castor running in the opposite direction, spins around, and fires another volley. There is complete silence as Archer drops his submachine gun and trades it for his pistol, while Castor backs up against the opposite side of the mirror panel and quips that he doesn't know which he hates wearing worse: Archer's face or his body. He offers to trade their faces back and surrender, but Archer replies "You can't give back what you've taken from me." Castor then decides to go to Plan B: kill each other.
Archer and Castor each train a pistol on their reflection, trained at the other. Both men open fire simultaneously, bullets shattering the glass. Archer suddenly is thrown, a bullet hitting him in the side. The two continue to exchange fire until Loomis arrives with a Commando rifle in hand. Loomis fires on Archer, driving Archer up the stairway and sending Castor diving for cover.
Up on the roof, Pollux sees Archer arrive. He climbs up onto a vent, while Archer climbs onto a rope dangling from a crane. As Pollux raises his pistol and prepares to shoot, Archer slams into him, sending Pollux flying before crashing through the skylight. Down below, Castor takes cover as Pollux and lots of glass shards come plummeting towards him. Castor looks up, sees Archer dangling, and fires several rounds, sending Archer fleeing.
Castor then looks down and sees Pollux lying on the ground, dead. He immediately breaks down crying. Suddenly Loomis appears, and not knowing that he's talking to Castor, he asks him why he is shedding tears for the likes of Pollux Troy. Castor snaps with rage, raises his pistol and promptly shoots Loomis in the face. Castor then takes notice of Pollux's untied shoelaces. In brotherly fashion, he delicately reties Pollux's shoes and departs.
The next morning, Castor returns to his office, dazed. He blows off his secretary as she informs him that he has made TIME Magazine's "Man of the Year" segment, then sits down in his office chair to brood about Pollux's death. Seconds later, an agitated Lazarro comes in to inform him that after the unnecessary carnage from his shootout with Archer at Dietrich's apartment, he's terminating Castor's war on crime. Lazarro fails to see a hint of anger suddenly flash across Castor's face as he queries as to how Castor happens to suddenly know so much about his own men's movements. Seeing Lazarro clutch his chest from palpitations, Castor stands up, checks to make sure no one in the office is looking, and admits to Lazarro that he'll give the taxpayers a break, but he has something he wants to confess to Lazarro, something he knows the director won't like. He promptly snarls into Lazarro's ear his true identity, then knocks Lazarro to the ground with a cut to the back of the neck. As Lazarro lies on the floor, Castor punches him in the heart hard enough that it stops completely. Collecting himself, Castor calls his secretary to tell her that Lazarro has just suffered a fatal heart attack.
Archer, meanwhile, breaks into his own house, narrowly avoiding the police officers that Castor has had placed outside to watch for him, and enters as Eve is coming out of the shower. Eve naturally does not take it easily seeing her husband's worst enemy's face, but Archer is able to keep her from making any noise that could attract the attention of the police officers in the house. He explains to her the exact details of the assignment he had been sent away on, how he was given Castor's face through plastic surgery to get information about one of Castor's crimes. After telling her what has happened, he admits that while she doesn't have to believe a word he says, there is one way Eve can validate Archer's claims: Archer's blood type is O+ and Castor's blood type is AB-.
When Castor comes home from work that night, he finds Eve working at her computer. He notices that she is looking tense and realizes that Archer has visited her and told her about him. Once Castor is asleep, Eve quietly and stealthily injects a needle into his left arm and draws some of his blood. She then sneaks out of the house and drives over to the hospital. Once there, she puts a couple of blood drops onto a plate and runs it through a hemoglobin test. She gasps as the results come back that say her sample is AB-, meaning she has been sleeping with Castor. Just then, Archer comes into the room, still clutching the bullet wound Castor gave him at Dietrich's apartment. Eve suddenly draws a revolver on him, saying she doesn't know who to trust. Archer realizes that she's holding his backup service weapon. Although Eve still appears skeptical of Archer's story, once he tells her the story of how they had their first kiss, she eventually realizes the truth. However, once all this is done, Archer promises to make it up to her and Jamie for all the neglect of emotions he put them through.
Eve then sets forth on stitching up Archer's wound in the emergency room. Archer is aware that Lazarro has died, and also knows that the chain of succession means that he technically becomes the new acting director of the Los Angeles field office. As Castor is in Archer's place, that makes him virtually untouchable. Eve tells him that won't be the case the next day, as Castor will be at Lazarro's funeral. Archer tells Eve to get herself and Jamie away from Castor as soon as possible. Eve is not sure, as she can handle an excuse for Jamie, but she's expected to go to the funeral as well, and if Castor doesn't see her, he will be suspicious. Almost as if on cue, there is a commotion outside. Aware that Eve has snuck out, Castor has arrived with Leo and Lars and is scouring the hospital looking for Archer. Eve quickly hides Archer as Castor pulls back curtain after curtain looking for his foe. When he pulls back the curtains around Eve, to his disappointment he finds her apparently in the middle of attending to a burn patient. She makes up a story about being on-call for that night. Castor apparently accepts her story and departs with his thugs. Once out of earshot from Eve, Castor quips, "Lies, deceit, mixed messages... this is turning into a real marriage."
The next day, Sasha and Archer track Castor to Lazarro's funeral, where Castor is holding Archer's wife and daughter Jamie hostage. Castor reveals that Michael's death was an accident and he was trying to kill Archer himself. However, he took it personally and advises him to either kill himself or let it go. Archer tells him no father would let go until the one responsible paid for it with his life. Castor replies neither would a brother. Sasha retorts not even a sister and gives Archer (as Castor) the gun. With Eve caught in the middle, everyone is engaged in a Mexican standoff. A gunfight then ensues in which Sasha and all of Castor's minions are killed. Having taken a bullet to save Archer, Sasha begs him not to let Adam grow up to be a criminal. Archer agrees to keep his promise to her as she dies in his arms and Eve feels sorry for her.
Castor and Archer engage in both a gun battle and hand-to-hand fight, with Archer gaining the upper hand. Jamie finds a gun and shoots at Archer (as Castor), believing him to be the real Castor, and wounds him in the shoulder, allowing the real Castor to break free. He takes Jamie as his hostage and licks her face as he mentions peaches. However, she gets him to let her go by stabbing him in the leg with the balisong, ironically a trick which he taught her earlier himself. Eve comforts her as Castor makes his escape by shooting two FBI members as Archer pursues him.
Castor manages to escape in a boat, pursued by Archer. After a lengthy chase both Archer and Castor's boats are destroyed and they are thrown ashore by an explosion resulting from their boats' collisions. The two engage in a final hand-to-hand confrontation which results in Archer eventually prevailing by killing Castor with a spear gun, (which leaves Castor in the same position as the statue shown earlier of Jesus on the cross) but not before Castor tries to destroy Archer's face (on himself) to prevent Archer reclaiming it.
Eve is able to explain the entire situation to the FBI and successfully convince them of Archer's true identity. Archer is then taken to the hospital where a team of Washington D.C.'s finest doctors does his surgery and his face is restored, with the exception of his chest scar which served as a reminder of the loss of his son as he doesn't "need it anymore", due to Castor's death.
After the restoration surgery, Archer (once again played by John Travolta) now wearing his original face and voice, comes home and hugs Eve and Jamie. Jamie apologizes for shooting him, but he tells her that she made the right decison because her bullet actually disloged the vocal microphone that turned his voice into Castor's. He is proud of the way she stood up to Castor when she stabbed him on his leg. Soon after, he brings Adam Hassler, Castor's son with Sasha, into his family, in order to fulfill his promise to her in not allowing him to grow up as criminal. Jamie acccepts him as her new brother and shows him to his new room. Eve agrees to adopt him with Sean, knowing that Michael has moved on and Adam can use a new home.