After an unnamed British secret agent retires from his position, he returns to his home in London to pack for a holiday. However, he is soon gassed and loses consciousness. When he awakes hours later, he finds himself in a strange community by the sea known only as the Village. In this place, no names are used and all phones, maps, taxis and other services are "only local." Number Six, as he soon becomes known as, is shown around the Village by its chairman Number Two, who explains that the information in his head is priceless and that he and his superiors want to know why he resigned.
Number Six discovers he has a new neighbour, Nadia, who soon becomes known as Number Eight. She is an Estonian secret agent who, like Number Six, is a prisoner in the Village because she resigned her job. Number Six befriends her and soon discovers that she knows the location of the Village: Lithuania. To increase both their chances, they decide to attempt to escape their prison together. To keep their plans a secret from Number Two, Number Six enters he Village arts and crafts exhibition competition. His entry entitled "Escape" is the inspiration for their plan to get back to London.
Not even Number 6's dreams are safe when Number 2 uses a drug to enter the Prisoner's mind and try to determine which of three individuals, designated A, B, and C, that Number 6 planned to sell secrets to.
It's Election Time in the Village, and Number 6 is encouraged to run for the office. Number 6 is skeptical that anyone can honestly rise to power, but soon finds himself swept into the election campaign.
Number 2 comes up with a scheme to break Number 6, by programming him with different likes and dislikes then convincing him that he is Number 12, brought to the Village to break the "real" Number 6.
The Village superiors are developing an electronic speedlearning process that allows them to place whatever information they wish in the human brain. The unwilling Professor developing the process is working with the mysterious "General," and Number 6 must thwart the scheme before the process is perfected.
Number 6 wakes up to find the Village abandoned. He makes a boat and escapes to freedom, only to fall victim to gunrunners. Upon reaching London, he must convince his superiors that the Village exists and that he can lead them back to destroy it once and for all.
Number 6's discovery of a dead man on the beach sets off a bizarre series of events which culminate in a Village carnival where everyone is masked... and no one can be trusted.
Number Six becomes involved in a living game of chess and discovers that the Queen has been programmed to fall in love with him and follow him while carrying a tracking device. The Prisoner allies with the Rook to use the Queen's tracking device to plan an escape.
When a young woman, Number Seventy-Three, takes her own life due to Number Two's efforts to break her, Number Six swears his revenge. He sets out on a campaign of misinformation in the hopes of pushing the already unstable Number Two over the edge. He plans to make the Village administrator think that he is an agent called D6 and that he is in the Village to spy on him.
Number Six uncovers a plot to assassinate Number Two. In the interest of avoiding reprisals against the community, he warns the Village administrator about it. However, Number Six is unaware that he being used as a pawn. The plot thickens further when the incumbent Number Two is replaced by a much older man due to retire within days.
Number Six is stripped of his protective status when the Village committee declares him "unmutual." When he refuses to cooperate, he undergoes mental treatment to fit in socially... but he soon realizes the entire thing is a ploy to break him.
Number Six finally escapes the Village... in another man's body. The Village authorities need him to track down a rogue scientist. Now Number Six must convince those who know him who he really is and find the scientist... who holds the key to restoring him to his true body.
Number 6 finds himself in a town from the American Old West. Unable to leave town, he has to take on the position of sheriff to protect a young woman, but refuses to take up a gun or explain his reasons why not.
In what may be a flashback, or an imaginary story, or a new ploy by the Village superiors, Number 6 is working as a secret agent to thwart Professor Schnipps and his lethal daughter Sonia.
It's a battle of wills when Number Two decides the only way to break Number Six is to enter into "Degree Absolute" with him. If Number Six triumphs, he will meet Number One. If he fails, he will die.
Having triumphed against the Village and those set to defeat him, Number Six is brought into the presence of the Assembly and its President. Before meeting Number One, the Prisoner must first watch as rebels Number Two and Number Forty Eight are put on trial for their acts of rebellion, then engineer one final escape.