In this story of Cold War espionage in a divided Germany, Alec Leamas is a British secret agent who becomes a double agent in order to bring down the head of the Communist intelligence agency in East Germany. All goes according to plan until Leamas finds himself before a secret tribunal that seeks to expose him as a British spy. His personal and professional loyalties come in to play as he realizes that nothing is how it seems. The novel explores the danger and intrigue of 1960s era Cold War espionage and the individuals caught up in it.

Alec Leamas is the head of British Intelligence in West Germany and oversees the spy missions in East Berlin. When his agent, Karl Riemeck, is killed crossing the border into West Berlin, Leamas returns to London to explain the situation to his boss, Control. Leamas expects to be fired but instead Control gives him a new and complicated mission to bring down the head of East German intelligence, Mundt.

Leamas begins to put the mission into practice. He appears to be slipping into a drunken and desolate state. He loses his job in the Banking Section of British intelligence through a fake embezzlement scam. After a series of low-level jobs, he takes a job at a library, where he meets Liz. Liz is a member of the Communist Party. Liz and Leamas begin a relationship that he breaks off when it is time to begin the next phase of his plan.

Leamas picks a fight with a store clerk and ends up in prison. After being released from prison, Leamas is approached by Ashe, an East German agent. Ashe and his partner, Kiever, present Leamas with the terms of his defection. Leamas is taken to Holland, where Peters interrogates him about everything that he knows about how British intelligence is organized. They are most interested in Rolling Stone, an operation for paying a secret agent through a complicated series of bank deposits abroad.

Leamas continues on to East Berlin, where he meets Fiedler, the second in command of East German intelligence. Fiedler is interested in using Leamas' evidence from Rolling Stone to show that Mundt is the secret agent that is working with British intelligence. Fiedler calls for Mundt's arrest and a Tribunal is called to investigate the case. At the Tribunal, Mundt claims that Leamas is a double agent working for Britain. Mundt calls Liz as a witness to prove his claims. The Tribunal sides with Mundt and arrests Fiedler for making the accusation.

Mundt assists Leamas and Liz in their escape from prison. They drive away from the prison and make their way to the border. When they reach the border, they have to climb a wall. While they are climbing the wall, the searchlights locate them. The guards shoot and kill both Leamas and Liz before they are able to escape into West Berlin.