The story opens in Lapland at the funeral pyre of Jerry Cornelius's father, a Nobel Prize-winning scientist who has developed the "Final Programme"—a design for a perfect, self-replicating human being. Jerry Cornelius, playboy physicist and dashing secret agent, is in attendance. Afterwards he is questioned by Dr Smiles, who wants to retrieve a microfilm which he knows is in the Cornelius family home in England. Cornelius, a conspicuous counter-culture dandy with addictions to chocolate biscuits and alcohol, threatens to blow up the family house. Flashbacks to Jerry's conversations with Professor Hira about the Kali Yuga inform the narrative, providing a philosophical background of the world in its final days. In various scenes, we learn that the Vatican no longer exists, that Amsterdam has been razed to ash, and we see Trafalgar Square in a post-apocalyptic scenario of wrecked cars piled atop one another.
Back in the UK, a group of scientists led by Dr. Smiles and the formidable Miss Brunner (who consumes her lovers) try to persuade Cornelius to locate the microfilm containing his father's Final Programme. Jerry learns from his family servant that his sister Catherine has been imprisoned by his evil, drug-addicted brother, Frank; Frank has Catherine held captive in their family home, and has addicted her to drugs for unspecified reasons. Jerry, whose relationship with Catherine is implied to be incestuous, instructs his servant John to smuggle Catherine to the lodge on the property's grounds; he will "take care of Frank". He consults Major Wrongway Lindbergh, who supplies him with a high-powered jet, and his old friend "Shades" who can supply him with napalm.
The attack on the old house commences. The house is protected by a sound system which induces pseudo-epilepsy, but Jerry and the others get inside unharmed. They fight their way past many traps including poison gas and a lethal chessboard. Jerry finds John fatally wounded by Frank. John confesses before dying that Catherine has not been freed and that Frank has returned her to the bedroom. Jerry finds and confronts Frank, and a needlegun fight ensues. In the confusion, Catherine is accidentally killed by Jerry. Jerry is wounded, and Frank falls into the hands of Miss Brunner. She forces him to open the vaults, but he outsmarts her and escapes with the microfilm.
After Jerry recuperates from the poison of Frank's needles, he meets with Miss Brunner. She introduces him to her new lover, Jenny. They plot to recapture Frank. Jenny is induced to play piano naked in Jerry's flat, where she is consumed by Miss Brunner. Frank has set up a meeting to sell the microfilm to Baxter (Patrick Magee); Jerry and Miss Brunner track them down. Miss Brunner consumes Baxter. Another fight with Frank ensues, and Frank is killed. Miss Brunner and Jerry return to Lapland by hot-air balloon with the recovered microfilm.
The scientists put the Final Programme into operation: the process requires that Miss Brunner be combined with another person to form a hermaphroditic being. Brunner chooses Jerry over the scientists' intended subject, Dmitri, and she traps Dmitri in a lethal steambath. Dmitri escapes Brunner's trap and fights Jerry, who is severely wounded. Brunner intervenes at the last moment, shooting Dmitri but not killing him. The scientists, working against time, scramble to re-calibrate their experiment for Jerry, who is placed inside a large chamber with Brunner. As the process reaches its climax, the two subjects are bathed by solar radiation and blur into each other. A single being emerges from the chamber. The scientists and Dmitri confront the creature. Unseen at first, the being speaks with Jerry's voice. The creature does not know if it is a Messiah, but is sure that its creation means the end of an age. When seen from the onlookers' perspective, the being is Jerry Cornelius, his body now altered to appear as a hunched over, pre-modern hominid. Cornelius leaves Brunner's hidden base and observes that it is "a very tasty world".
Michael Moorcock has said that he originally envisioned space-rock band Hawkwind as providing the music for the entire film, and also appearing in the scene with the nuns playing slot machines where Jerry is trying to buy napalm. Hawkwind, and Moorcock himself, can in fact be glimpsed briefly in this scene right at the back of the set. Director Robert Fuest, however, did not like Hawkwind and had music with a jazzy feel placed into the film. Moorcock has also praised the acting performances in the film, and commented that it was only when he told the actors it was supposed to be funny that they delivered lines with more of his intended black humour. 
According to Moorcock, the film was released as the top half of a double bill with Confessions of a Chinese Courtesan. Later in the run, The Final Programme was moved to the bottom half of the bill.
Baird Searles found the film "an almost unmitigated disaster," with "an ending so inane that you will want your money back even if you wait and see it on television."
On its DVD/Blu-ay release in the UK in 2013, The Guardian wrote " Director Robert Fuest was responsible for the pop-surrealism of The Avengers and the twisted art deco of Vincent Price's Dr Phibes movies, and here he makes sure every frame looks stunning, throwing so much in to please and confuse the eye, often at the cost of narrative coherence. But who cares when the movie is full of cryptic, sly humour and endlessly inventive imagery, such as an amusement arcade where nuns play fruit machines as the world ends."Jon Finch as Jerry Cornelius
Jenny Runacre as Miss Brunner
Hugh Griffith as Professor Hira
Patrick Magee as Dr. Baxter
Sterling Hayden as Major Wrongway Lindbergh
Ronald Lacey as Shades
Harry Andrews as John
Graham Crowden as Dr. Smiles
George Coulouris as Dr. Powys
Basil Henson as Dr. Lucas
Derrick O'Connor as Frank
Sarah Douglas as Catherine
Sandy Ratcliff as Jenny
Julie Ege as Miss Dazzle
Gilles Millinaire as Dmitri
Sandra Dickinson as Waitress
The film was released on DVD and VHS formats in the US in 2001 by Anchor Bay Entertainment. The Anchor Bay DVD featured a remastered print of the film, which could be played with an audio commentary featuring director Fuest and star Runacre. Other special features on this DVD included the American theatrical trailer and TV spot, and an insert replica of the British poster. The Anchor Bay DVD is now out-of-print and hard-to-find, with existing copies retailing up to £100 on sites such as Amazon.
On 7 October 2013, Network Distributing released the film on DVD in the UK. The Network DVD is presented in a brand-new transfer from the original film elements, featuring both the 1.77:1 theatrical ratio and the full frame, as-filmed version of the main feature. Special features include original theatrical trailers, an Italian title sequence, image gallery, and promotional material in PDF format.