A British secret agent drives to his headquarters and storms into the office of his superior. He angrily confronts the man, then tosses down a letter and leaves. As he returns home, he's unaware that he's followed by a black car. At the headquarters, the agent's file is x'd out and filed in the "resigned" cabinet.
The agent returns to his home in London and packs for a vacation. He's unaware of a man in a black coat and top hat emerging from the black car and going to his doorstep. A stream of gas pours through the key hole and the agent passes out.
When he wakes up, the Prisoner finds himself in a strange cottage. he looks outside and sees a quaint village with buildings made up in different styles of architecture. Running outside through the empty streets, he makes his way to a bell tower to survey the area and finally spots people emerging for their morning tasks. He goes to a café and asks the woman where he is, and she responds that he is in "the Village." the Prisoner asks for the police and is informed there isn't any. She directs him to a phone but the operator asks for his number and tells him if he has no number, he can't make a call. She then informs him that the phone is for local calls only.
The Prisoner checks out a directory map marked with numbers and summons a taxi driver. The taxi driver greets him in French and wonders if he's from Eastern Europe, noting the Village is "very cosmopolitan. She informs him the taxi is a local service and drives the Prisoner around the town, then informs him that he owes her ten "units." but allows him to pay later.
Next the Prisoner goes into a store and tries to buy a map showing his location. However, the store owner only has local maps, in black and white and color. None of them give specific proper nouns to any location in the Village. The Prisoner goes outside and sees a maid working in his cottage. He goes in and returns, discovering that his cottage is now labeled "Number Six." The door opens for him automatically. As he enters, the pone rings and the operator asks if she has contacted Number Six. A male voice then identifies himself as Number Two and invites the Prisoner to breakfast at the Green Dome.
The Prisoner arrives at the Green Dome and enters a huge chamber where Number Two is waiting for him. He offers his visitor breakfast, knowing exactly what he wants, then explains that the information in the Prisoner's head is priceless. Their superiors want to know why the Prisoner resigned, but the Prisoner insists they have no business doing so and his life is his own. Number Two goes over the Prisoner's entire life on file, but notes there are occasional times when he disappeared and they want to know what he did on those occasions.
Number Two offers the Prisoner a deal: he gives them the reason for his resignation in return for a position of authority. The Prisoner refuses, insisting they can't hold him. Number Two disagrees and takes him on a helicopter tour of the Village, pointing out the buildings of import. The Prisoner is unimpressed. They land and Number Two shows him the old people's home, noting that many of the residents live out their lives in the Village. As they go through the town square, Number Two calls out for everyone to freeze. One man refuses, and a large white sphere appears atop the fountain then attacks the man, suffocating him. Number Two then takes the Prisoner to the Labour Exchange and puts him through an aptitude test, which the Prisoner refuses to participate in. He storms off, and Number Two admits that they may have a challenge on their hands.
The Prisoner returns to his flat to find the maid clean up the place. He tells her to get out then stalks around his quarters like a caged tiger. In the background soothing music plays on a speaker. The Prisoner finally destroys it and a gentle alert goes out requesting an electrician. The maid returns to get an item she forgot and tells him there's no way to stop the music from playing. When he interrogates her, she admits that she has lived in the Village as long as she can remember, and her parents lived there before her. She breaks into tears and claims "they" will know she's said too much. She admits that she tried to make a deal with the Village superiors to get information from him in return for his freedom. The Prisoner scoffs at the idea that they would let her go once she learned what was inside her head. Unimpressed by her tears, he tells her to get out.
Number Two is comparing notes with the Village Supervisor and notes that due to the Prisoner's importance, they'll have to handle him carefully.
An electrician arrives with a replacement speaker. The Prisoner claims to be going for a walk, and tries to make a break for it. He goes through a yard of statues with electronic monitors for eyes, as the Supervise watches from the security centre. The white "guardian sphere" bounces back as the Prisoner ducks for cover but then when he moves off, it tries to intercept him. He runs to the beach where two of the village's security force ("Guardians") run him down. He defeats one then boards the cart and knocks out the other. However, the guardian sphere intercepts him, knocking him off of the cart and stunning him.
The Prisoner wakes up in the Village hospital and finds that his bedmate is Cobb, a fellow spy. They know each other and Cobb admits that he doesn't know where he was or how he was brought there. A doctor arrives and the Prisoner demands to be released. The doctor turns down his request and administers a basic physical, determining the Prisoner is okay after his "encounter" with the guardian sphere. As they return to the Prisoner's bed, an alert goes off. They discover that Cobb has leapt to his death out of a window.
The next morning, the Prisoner is released from the hospital but discovers that his old clothing has been burned and he's been given typical Village clothing. He's also given ID papers labeling him "Number Six." Going to the Green Dome, the Prisoner discovers that the original Number Two has been replaced by an entirely new man, who takes a much less conciliatory tone with him. The Prisoner demands to know what was done to Cobb but the new Number Tow insists that it was necessary, then asks the Prisoner why he resigned. The Prisoner refuses to answer, and as he leaves Number Two addresses him as "Number Six," then notes that extreme measures against him won't be necessary… for now.
Number Six returns to his flat then sees a procession taking Cobb to the Village graveyard. He spots one woman moving behind the procession and crying. He approaches the Woman and informs her that he knew Cobb as a friend. She is suspicious but agrees to meet Number Six later. They rendezvous at a Village concert and she claims to have a way to escape, and that she was trying to help Cobb escape. She has an electro-pass, given to her by a friendly helicopter pilot, and she's willing to give it to Number Six. He agrees to meet with her later and she departs. He secretly follows the Woman and discovers her going to the Green Dome. Inside, she discusses the matter with the new Number Two, who assures her that Cobb's death won't reflect badly on her. He then gives the file on her new assignment: Number Six.
Number Six is at their rendezvous spot near the helicopter pad when the Woman arrives. She gives him the electro-pass and he confronts her over her meeting with Number Two. She insists that she is just playing along, didn't betray Cobb, and doesn't plan to betray him, then says that he hast o leave before it's too leave.
Number Six goes to the helicopter and the electro-pass, similar to a wristwatch, activates. The guardian sphere hovers ominously but responds to the electronic password and lets Number Six by. He boards the helicopter and flies away. However, just as he's clear of the Village, Number Two takes control of the helicopter by remote control and brings it back to the Village. Number Two then turns to… Cobb, and informs him that their mutual masters will be pleased. Cobb, making his departure, wishes Number Two well but warns that Number Six will be hard to break.
Number Six is escorted from the helicopter and the guardian sphere follows him as he returns to… the Village.