A bearded stranger (Jodorowsky), clad in black leather, rides his horse on a sandy plain. His naked son sits behind him. The father says "Now you are a man. You are seven years old. Bury your favorite toy and your mother's picture." The burial consists of propping these symbols up in the sand. The father and son come to a town, a scene of carnage, a town of corpses and entrails; animals, children - everyone has been butchered and the waters flow red with blood. The bearded man in black leather becomes a gunfighter out of the old west. An avenger, he tracks down the murderous bandits and proceeds to castrate their warlord. With the words, "Destroy me. Depend on no one," he leaves his song with a group of monks that he has liberated and takes up with the warlord's mistress.

The man in black and the woman whom he calls "Mara," go into the desert where she convinces him that he must conquer four masters who dwell there. The masters are different types of holy men, who are subject to contests, four enigmatic mind games of a sort. The characters speak in high-flown riddles, a kind of Zen, "Confucius say" speech along the lines of "the desert is a circle." The man in black wings his contests by chicanery and realizes, too late, that he has truly lost. He cries out to ask why God has forsaken him. Meanwhile, Mara has been joined by a sadistic lesbian in butch black couture. As the stranger thrashes about in guilt for his crimes, battering himself against walls that crumble, the lesbian comes at him and pumps him full of bullets. He keeps walking, arms outstretched and with stigmata on his hands and feet, until Mara shoots him down. The women kiss with tongues lasciviously extended and leave him for dead. A group of dwarfs and cripples cart his body off.

Years have passed -- as many as two decades. He sits as a holy man in a cave in a mountain tended by a worshipful woman dwarf. Spiritually reborn, his beard and heave shaved in penitence, he pledges himself to liberate the tiny group of cripples trapped in the mountain, imprisoned there by the people of the nearby town to safeguard them from having to see the malformed results of generations of incest. The holy man begins work on a tunnel and, because of his height, he is able to scale the walls of the cave, coming and going and taking the female dwarf with him. They go into the town and we are, once more, back in a Western. The town is a synthesis of the gambling, whoring saloon towns of Western movies, with a lurid catalog of evils: blacks are sold as slaves and branded, accused of rape by lecherous women. They are lynched and so it goes. The penitent cleans toilets in the town jail and becomes a clown - God's fool - in order to buy dynamite to blast the mountains apart. Then he and the female dwarf go to the church where the parishioners pass the time playing Russian roulette, they ask to be married. The priest turns out to be his abandoned son. The three of them go back to the mountain to free the cave people. Once free, however, the crippled, helpless little monstrosities who are like deformed Munchkins rush to see the wonders of the town that is finally accessible to them. The townspeople meet them with rifles and shoot them down. By the time the holy man arrives, they have all been massacred. He yells and he, too, is shot. Again and again he is shot but he keep coming towards the townspeople like a Golem. Full of holes, he picks up a gun and, once more the avenger, retaliates by slaughtering the townspeople. Seated cross-legged, he soaks himself in kerosene for a lamp and immolates himself. A new holy family - his song, now bearded and dressed in black like his father before him and the dwarf widow, carrying their newborn baby, ride away into the fulcrum from which the movie began.