The peaceful people of Gandahar are suddenly attacked by an army of automatons known as the Men of Metal, who march through the villages and kidnap their victims by turning them to stone. The resulting statues are collected and then transferred to their base. At the capital city of Jasper, the Council of Women orders Sylvain to investigate. On his journey, he encounters the Deformed, a race of mutant beings who were accidentally created via genetic experimentation by Gandahar’s scientists. Despite their resentment, they are also threatened by the Men of Metal and offer to help Sylvain.
Sylvain later saves Airelle, a Gandaharian woman. Together they discover the Men of Metal’s base, where the frozen Gandaharians are taken through a large portal and are seemingly assimilated into more Men of Metal. The two stow away on a nearby boat which heads towards the middle of the ocean where they encounter Metamorphis, a giant brain. Sylvain and Airelle are captured and confronted by Metamorphis, who tells them that although the Men of Metal believe that he is their leader, he did not create them nor order their attack. He states that he does not want to see Gandahar fall, and that he needs time to figure out the connection between him and the Men of Metal. He then returns Sylvain and Airelle to Jasper where they learn that Metamorphis, like the Deformed, was also an experiment by Gandaharian scientists. Due to his rapid growth and increasingly violent behavior, he was abandoned in the ocean. Sylvain is ordered to kill Metamorphis with a special syringe. Sylvain returns to Metamorphis, who maintains his innocence but reveals that the Men of Metal come from the future via the portal Sylvain saw earlier. He then urges Sylvain to kill him in a thousand years, as the syringe would have no effect on him now. A skeptical Sylvain agrees and Metamorphis puts him into stasis.
A thousand years later, Sylvain awakens just as they had agreed. He comes across the Deformed, who explain the true nature behind the Men of Metal: Due to Metamorphis’s now advanced age, his cells can no longer regenerate, which drove him to create the Men of Metal and order them to go back in time to capture the Gandaharians so he could absorb their cells to continue living, killing the Gandaharians in the process. The Deformed, however, were abandoned as they were considered undesirable. Sylvain and the Deformed then agree to work together. The Deformed fight off the Men of Metal and rescue the remaining Gandaharians while Sylvain goes to face Metamorphis alone. The Deformed destroy the reservoir supplying Metamorphis with new cells, distracting him long enough to let Sylvain inject the syringe into Metamorphis which kills him. Sylvain, along with the Deformed and the Gandaharians escape through the portal back to their time.
Voice actors for the original French version included Pierre-Marie Escourrou, Catherine Chevallier, Georges Wilson, Anny Duperey, Jean-Pierre Ducos, and Jean-Pierre Jorris.
Among the actors providing the voices for the English-language version were Glenn Close, Jennifer Grey, Terrence Mann, Teller of Penn and Teller, John Shea, Bridget Fonda, David Johansen, Earle Hyman, Earl Hammond and Christopher Plummer.
The animation was in colour and ran for 83 minutes. Production work was done by SEK Animation Studio of North Korea. The film is notable for its strange scenery and exotic flora, fauna, and bizarre inhabitants. The design was by the French comic book artist Caza.
This version was directed by Harvey Weinstein and produced by Bob Weinstein through Miramax Films itself, while noted science-fiction author Isaac Asimov made the revision of the translation. The English title is a translation, not of the original title, but of the original tag line "Les Années lumière" (The Light Years) as seen on the French poster.The English version does not contain most of Gabriel Yared's soundtrack for the original version of the film. New music was produced for certain sequences in the English-language version of the film, these new pieces were created by the combined efforts of: Jack Maeby, Bob Jewitt and Jim Klein.
A certain scene in the English version was edited due to sexuality – the scene where Airelle and Sylvain are in the nest. In the uncut version, Sylvain is shown removing his shirt, later, he and Airelle are shown lying nude in the nest at night, seemingly after having been intimate with one another.
A European DVD release of Gandahar, in French with English subtitles, was released in October 2007  by Eureka!'s Masters of Cinema label. There are currently no plans for a Region 1 DVD release.