The Supervisor, with the Butler accompanying him, takes Number Six onto an elevator and descends into a lower underground passageway. The Supervisor takes him down the hallway to a mannequin wearing a suit: Number Six's clothing from his previous life, provided to make him more comfortable. They then escort Number Six down a passageway with jukeboxes playing "All You Need is Love" by the Beatles. Number Six is led into a large cavern where the Assembly is gathered: men in robes and masks labeled Nationalists, Reactonists, Therapy, Defectors, and so on. They applaud Number Six and the President of the Assembly, dressed as a judge, welcomes Number Six to the gathering. The Supervisor dons a similar robe and mask while the Butler stands at Number Six's side. The President explains that they have gathered to resolve undirected revolt and rebellion within the community. He introduces Number Six to the Assembly, but says that since he was won his freedom he is now to be addressed as "Sir." The President asks Number Six to take a seat in the chair of honor and observe as they go through the preliminaries of transfer.
The portable kitchen/cage from the Embryo Room is lowered into the cavern and opened. The President has a team of doctors resuscitate the dead Number Two, as a glowing mechanical eye labeled "1" attached to a metal cylinder watches the proceedings and seems to silently communicate with the President. The doctors cut off Number Two's beard and trim his hair.
The President says they are faced with three forms of revolt. The first rebel is raised into the chamber from a tube leading below. The man, dressed in a black suit and white frilled suit but with a flower on the hat, is Number Forty-Eight. He speaks in hippy slang and tries to sing. The Assembly panics and the President calls for order. He then has the guards release Number Forty-Eight, while speaking of the undirected rebellion of youth. Number Forty-Eight rings a bell tied around his neck and bursts into song, then runs around the chamber. The doctors and guards are powerless to stop him but Number Six finally addresses him simply as "young man," attracting his attention and bringing him to a stop.
The President thanks Number Six for his aid but says they must follow the protocol. The mechanical eye informs the President to proceed. The President and Number Forty-Eight chant back and forth, the President emulating the rebel's youthful language. He demands that Number Forty-Eight confess but the rebel bursts into song again and the Assembly and guards join in. Even the President chants along, but then declares Number Forty-Eight guilty. He then reads the charges: questioning authority and refusing to acknowledge his number. He asks for Number Six's opinion, and Number Six says he has no comment. The President has the guards return Number Forty-Eight to the tube and orders him held pending Number Six's inauguration.
The next rebel the President brings forth is Number Two. He is surprised that he's been brought back to life and says he's a new man. He congratulates Number Six and expects the Butler to serve him, but the Butler refuses. He then talks of how the community abducted him and used his considerable skills to their benefit, and wonders how they brought him back to life. Number Six asks him if he's ever met Number One. Number Two finds the question amusing, but then notices the mechanical eye. He challenges it, claiming it hypnotised him, but he refuses to be hypnotised any longer. He throws away his badge and the eye overloads. The guards take Number Two to the President, who proclaims him guilty and orders him to be held. Number Two is placed in a tube and lowered downward, laughing heartily the entire time.
The President explains the second form of revolt: a member of the establishment biting the hand that feeds him. He then turns to the third form of revolt: the pure unadulterated quest for freedom against the establishment. He acknowledges that Number Six is just such a revolutionary and shows him an image of his flat in London and his car. He says Number Six must now choose to return to his former life, or lead them. The President gives him a passport and a million pounds to facilitate his return to his life if he so chooses. Number Six questions the proceedings and the President says that now that he has proven he is a true revolutionary, they need him to lead them. However, he asks Number Six to address the Assembly before making his decision.
Number Six takes the stand and tries to address the Assembly. As he begins to speak, saying, "I...", the Assembly chants "Aye!" repeatedly. He tries repeatedly to silence them and speak his mind, but each time they interrupt. Number Six begins to panic and the President calls for silence. He thanks Number Six and then prepares to grant his wish: a meeting with Number One. He takes Number Six into the lower levels and into a hallway where Numbers Forty-Eight and Two are confined in glass tubes. The Butler escorts Number Six up a spiral stairway to a control room with globes in the center of the room. A masked figure, wearing a robe marked "1" and holding a crystal orb turns to greet Number Six. Number Six takes the globe and drops it, then pulls away the figure's mask to reveal... a chimpanzee, chittering away. Number Six pulls away that mask to reveal... himself. The figure laughs at him and Number Six laughs back, then chases his doppelganger around the room. Number One climbs up a ladder, laughs mockingly one final time, and then closes and locks the hatch.
Number Six grabs a fire extinguisher and moves carefully downstairs, catching the attention of the Butler. The two of them attack the robed minions, then take their robes and free Numbers Forty-Eight and Two. They lure the other guards in and defeat them, then Number Six goes back up to the chamber and sets the controls to overload. The President notices the systems overload and declares an emergency as the mechanical eye's cylinder starts to overheat. The Assembly panics and Number Six and his allies storm the chamber, opening fire on the guards and killing them. The President orders an evacuation of the entire Village. People flee in panic, escaping by helicopter.
Number Six and his allies get into the kitchen, which is revealed as the back of a truck. The Butler drives them away and smashes through a gate, bringing them to the A20 in England. Behind them, the metal cylinder, a missile silo, launches its contents. The missile soars up into the sky while Rover melts into nothingness.
Number Six and his allies throw away their robes and dance. The Butler pulls over and Number Forty-Eight gets out, waves them farewell, and starts walking back the way they came, thumbing a ride.
The Butler proceeds to London and they drop off Number Two. He confidently walks toward Parliament.
Number Six and the Butler abandon the truck and walk through London. After a brief conversation with a policeman, they run through the streets and take a bus to Number Six's flat. Number Six gets into his car and prepares to drive away, but pauses as a black hearse goes by. As he leaves, the Butler goes to the flat and the door opens automatically.
Number Two, now dressed in an impeccable suit, enters the Peers' entrance of the Palace of Westminster.
Number Six drives down a familiar empty highway as thunder booms above him.