A Christlike figure wanders through bizarre, grotesque scenarios filled with religious and sacrilegious imagery. He meets a mystical guide who introduces him to seven wealthy and powerful individuals, each representing a planet in the solar system. These seven, along with the protagonist, the guide and the guide's assistant, divest themselves of their worldly goods and form a group of nine who will seek out the Holy Mountain, in order to displace the gods who live there and become immortal.
Director's son Brontis Jodorowsky, talking about the deleted scene:
..Oh, and well, in The Holy Mountain I was going to appear in, but they cut my scene because a girl of my age was naked in bed. Only her butt could be seen, but the mother tried to get money saying that her daughter was traumatized, but I knew her because she was in my school, and she were not traumatized. Well, in the end she did not win the process, and they did not give her money, but the judge said they had to cut the scene and I did not show up.