Lapland, an unspecified point in the future during World War III. Jerry Cornelius, Nobel Prize winning scientist and international playboy, arrives by helicopter for the funeral of his father. He encounters Dr. Smiles, who is looking for a microfilm kept in the old man's house. Cornelius does not want to help; he is more interested in being reunited with his sister, Catherine.

Back in England, Cornelius learns that Frank, their drug addicted younger brother, is holding Catherine prisoner at the house. Planning his revenge, Cornelius buys a fighter plane and meets a contact at a pinball arcade to purchase napalm bombs. At the arcade, he encounters Dr. Smiles and his colleagues Powys and Lucas. He finally agrees to help them obtain the microfilm.

Meeting at an aerodrome, Cornelius plans the assault on his father's house with his new allies. He is introduced to Miss Brunner, a computer programmer, and Dimitri, her chauffeur. Miss Brunner is working on the Final Programme, which will collect the sum total of mankind's knowledge on computer. She reveals that the microfilm is vital to the success of the project. That night, Cornelius and the others break into the house, avoiding defensive strobe lights designed to induce epilepsy in any trespassers. He and Miss Brunner head off to deactivate any booby traps. Smiles, Powys and Lucas try to find the microfilm by themselves, but are driven into a hypnotic rubber maze by jets of poison gas. Cornelius rescues them from their trance.

Cornelius locates Catherine, who is being kept sedated in her bedroom. Frank arrives and a gunfight ensues, with both brothers using 'needle guns' - pistols that fire drug tipped darts. Cornelius is wounded, and accidentally kills Catherine while in the grip of a hallucination.

Miss Brunner captures Frank and forces him to hand over the microfilm by withholding his drugs. Frank tricks her and escapes by sealing himself behind a heavy glass partition.

Cornelius recovers from his mental and physical wounds at a nursing home. When he discharges himself, he is met by Miss Brunner, who takes him to a wrestling match at a restaurant. Later, accompanied by Jenny, Miss Brunner's assistant, they head for Cornelius's apartment to plan how to locate Frank and the microfilm.

At the apartment, Miss Brunner contacts her computer to work out Frank's most likely hiding place, while Jenny plays the piano. Miss Brunner makes love to Jenny and proceeds to completely absorb her. In the morning, Cornelius finds Miss Brunner playing the piano in exactly the same way that Jenny once did.

Cornelius and Miss Brunner head to Turkey in his fighter plane. They are following Frank, who has set up a meeting to sell the microfilm to Baxter, one of his father's oldest rivals. Cornelius chases after Frank, while Miss Brunner makes love to Baxter and absorbs him. Cornelius kills Frank in a shootout at an abandoned fort, and retrieves the microfilm from his body.

Miss Brunner examines the microfilm. It contains the necessary information to create the new Messiah, a hermaphrodite with all mankind's knowledge stored within two brains. It appears from the data that Cornelius is the ideal candidate for the procedure. She keeps the knowledge from him, but invites him to witness the execution of the Final Programme.

Cornelius and Miss Brunner arrive at an abandoned Nazi submarine base in Lapland, where the Final Programme equipment is housed. Dr. Smiles and his colleagues give Cornelius a guided tour of the facility. Meanwhile, Miss Brunner tries to kill Dimitri with poison gas, but he escapes.

Dimitri, who was to be the original subject of the Final Programme, hunts down Cornelius and, in a fit of jealousy, tries to kill him. Dimitri manages to wound him before Miss Brunner shoots him dead. She takes Cornelius to a chamber, and reveals to him that he will merge with her to become the Messiah of a new age. As they make love, the Final Programme is executed.

The Cornelius/Brunner hybrid, now resembling a Neanderthal, emerges from the chamber. The forces unleashed have killed Smiles, Powys and Lucas. The creature shambles off into a world that appears to have been finally destroyed.