Gandaharians, the peaceful people of Gandahar are attacked. But by whom? And by what? The Gandaharians are petrified by diabolical rays. The server Sylvain, the son of the Queen Ambisextra, is designated by the Council of Women to investigate this enemy; to find where it hides and pierce its weaknesses so as to destroy it.
With the aid of the "Deformed", a mutant people -- results of the flawed genetic experimentation of their Gandaharians ancestors -- Sylvain goes in search of indices and becomes victimized by a villainous army of black robots. Enclosed in an egg-prison, he meets Airelle, a Gandaharian woman who he quickly falls in love with. Both are freed thanks to the intervention of a Saurn, a huge monster that sweeps the legion of "Metal Men".
Following the enemy discreetly, they are led into a fortified city. They testify to the fate reserved for the prisoners. Through a strange luminous gate that leads nowhere, they are transformed into these terrible robots. Airelle and Syl discover that Metal Men follow a cult in the "Great Generator" that is found on the eccentric ocean. Their god wants to destroy the Gandaharians to put an end to their pleasure and lustful civilization. They stow away on a ship and disembark at its destination, which proves to be an immense brain. It explains that it does not wish the end of Gandahar and claims not to be the chief of the Metal Men. To prove its good faith, the Great Generator frees its prisoner and leads them to Jasper, the capital of the planet where refugees flock in order to escape the terrible robots.
Syl and Airelle learn from the Jasper's scientists that the Great Generator is nothing other than a flawed scientific project. The "Metamorphis" project aimed at creating an autonomous brain. Escaping their control it had been deployed on the eccentric ocean. Today it has returned against them. Gandahar generated its own assailants in unconsciousness.
Syl has to convince Metamorphis to cease the attacks against the Gandaharians and so he leaves Jasper to do so. However, he learns that the invasion comes directly from the future through the temporal gate (the one he noticed in the fortified city). Today invincible, Metamorphis asks him to suppress it 1000 years later, when it will have become weak. To help him to realize his destiny, the giant brain throws Sylvain in hibernation at the bottom of the ocean...
Spoiler ! the end of the story is revealed below…
When he wakes up, 1000 years have passed. Sylvain has decided to do what Metamorphis asked of him; to destroy it. Once more assisted by the "Deformed", Syl understands that the giant brain has become very old and that its cells have degenerated. He also learns that it now extracts its necessary energy directly from the bodies of the Gandaharians, who have become its slaves. Syl and the Deformed attack. After having neutralized the Metal Men, Sylvain puts an end to the brain and delivers the people of Gandahar from slavery. The peaceful people rush towards the temporal gate and go back in time 1000 years before any trace of the invasion exist.