A young woman enters Number Six's flat, unaware that a satisfied Number Two is watching her from the Observation Room. She approaches the sleeping Number Six but he's awake and aware of her. He grabs her before she can touch him and asks what she wants. She wants his help but he figures it's a trap and refuses. He tells her to get out. In the Observation Room, Number Two checks his watch and wonders if they timed the slow-release drug it correctly. The woman collapses and Number Six gets her to a couch… just as Number Two anticipated. However, when he learns that the Supervisor unlocked Number Six's door to facilitate her entrance, Number Two snaps at him, saying that Number Six will suspect a trap.
The woman recovers consciousness and Number Six judges from her pupil dilation that she was drugged. He agrees to listen to her and she explains that she's trying to prevent an assassination. She couldn't care less about the target but knows that the Village authorities will take reprisals against all of the Villagers. He points out that he's under constant surveillance and Number Two now knows about it. The woman explains that she's a "jammer." However, when she realises that Number Six doesn't believe her, she leaves before she can explain what a jammer is.
Number Two is considering the plan and wishing he had more time. He's interrupted by a call from his superiors, and is forced to make sure Number Six is involved to give their scheme credibility. Number Two orders a priority activity prognosis on Number Six and then meets with Number One Hundred. Number One Hundred is an undercover operative and assures Number Two that his target trusts him and has no idea who he really is.
As part of his daily schedule, Number Six poses for a portrait painting by the Artist at the Old Folks Home. The Artist mentions jammers and explains that they're involved in civil disobedience. They hatch imaginary schemes and leak them to the authorities. The authorities used to waste time and resources investigating them, but now keep a list of jammers and ignore their activities.
The Computer Attendant delivers the activity prognosis to Number Two. It is amazingly accurate, to the point where it predicts Number Six buying a bag of sweets. As it turns out, he randomly meets an old woman who doesn't have units to buy them so Number Six buys them for her. Checking Number Six's schedule, Number Two spots his weekly kosho practice and sends Number One Hundred to the gymnasium. While Number Six is sparring with his opponent, Number One Hundred switches Number Six's watch for a malfunctioning identical copy.
After the match, Number Six discovers that his watch isn't working and goes to the Village Watchmaker. As the elderly man goes out the back to fix the watch, Number Six notices a remote control device and the trigger item that it activates. The Watchmaker returns and dismisses the item as a toy. Number Six leaves and Number One Hundred arrives. He explains that they're letting Number Six know what they're up to so as to further confuse the authorities.
Number Six meets the woman as she arrives at the Watchmaker's shop. She wonders how Number Six discovered who she was and admits that she's the Watchmaker's Daughter. He points out that her father is working on the triggering device for a bomb and is starting to wonder what's going on. Number Two and his assistant watch, satisfied that everything is going according to plan and they should expect a visit from Number Six.
Number Six and the Watchmaker's Daughter confront the Watchmaker, who refuse to listen to them. He insists that the assassination is necessary and it may take reprisals by the authorities to wake up the Villagers. Number Six disagrees, warning that no one may survive to rebel.
Number Two and Number One Hundred believe that Number Six will soon come to warn Number Two. Number Two sets up cameras throughout his office to record sound and audio. Number Six arrives at the Green Dome, passing Number One Hundred on the way in. He explains about the assassination plot to Number Two, who feigns disinterest and claims that it's another scheme by the jammers, who have fooled Number Six. Number Six storms off, unaware that he was recorded. Number Six meets with the Watchmaker's Daughter and they realise they'll have to stop the assassination on their own. Meanwhile, the Village authorities make an announcement that Appreciation Day will be the day after tomorrow and Number Two will give a speech as they unveil the Appreciation Monument. That night, they sneak into the Watchmaker's shop and find an explosive replica of the Great Seal of Office, which is worn by Number Two at ceremonies.
The next day, Number Six goes to visit Number Two with his new testimony, only to discover that there is a "new" Number Two. This older Number Two explains that the Number Two that Number Six has been dealing with is his interim replacement while he has been on leave prior to his retirement. The New Number Two warned him about Number Six's claims and has labeled him as a jammer because of his many reports. Number Six doesn't know what he's talking about and the Retiring Number Two plays first a legitimate tape of Number Six confronting the New Number Two, and then faked tapes of Number Six warning other interim Number Twos. Number Six realises he's been set up and warns that the authorities took steps to guarantee he wouldn't be believed. As he goes, the Retiring Number Two notes that he will be handing over power to the New Number Two at the Appreciation Day ceremony.
Number Six and the Watchmaker's Daughter meet at a café and conclude that the authorities deliberately set out to discredit him, as he's the only person who might have convinced the Retiring Number Two of the plot against him. They notice Number One Hundred seated nearby and the Watchmaker's Daughter recognises him as her father's co-conspirator, but Number Six saw him with the New Number Two and realises that he's manipulating the Watchmaker. Meanwhile, the Retiring Number Two is monitoring their conversation and begins to believe Number Six's claim. He asks the New Number Two's assistant to provide him with the tapes of Number Six but the assistant claims they no longer exist… confirming the Retiring Number Two's suspicions.
Number Six and the Watchmaker's daughter conclude that the authorities typically dispose of their underlings upon retirement and then frame others - in this case, the Villagers. Number Six goes to the Retiring Number Two again with his new conclusions and the man admits he believes him, although he never thought it would happen to him. He resigns himself to the inevitable but Number Six isn't interested in him: he doesn't want the Villagers to suffer reprisals. He notes that the authorities plan to blow up the Retired Number Six and leaves.
The Appreciation Ceremony begins as planned and both Number Twos arrive for the presentation of the Great Seal to the successor. The New Number Two has a radio transmitter hidden in his thick-rimmed glasses and checks in with Number One Hundred, who is watching to make sure the Watchmaker unwittingly performs his part in the plan. Number Six and the Watchmaker's Daughter are searching the crowd for her father and spot him in the bell tower. They go upstairs as the Retiring Number Two dons the Great Seal. Number Six manages to get the Watchmaker to drop the detonator remote. When the bomb doesn't go off, the New Number Two sends Number One Hundred to investigate. He fights Number Six for the remote and after a struggle, Number Six emerges triumphant.
On the podium, the Great Seal is transferred to the New Number Two. Number Six steps up and gives the remote to the Retiring Number Two, and tells him to get away so the Villagers aren't punished for his death somewhere else. The Retiring Number Two takes his chances and flies as faraway as he can in a helicopter. The New Number Two tries to stop him until he sees he has the remote. Number Six shakes his hand to keep him from removing the Great Seal and the Retiring Number Two flies away.