Jodorowsky is full of bullshit, but that doesn't mean his work is worthless. I loved The Incal not because it made any kind of sense (because it totally doesn't). It's a journey over destination kinda deal. Seriously. That comic was inspired by the tarot, and it works as a tarot deck – a heap of symbolic images to which YOU supply the meaning. Similarly with this film – you don't watch it, it watches you. El Topo mashes together myth and pulp into these fantastical and allusive scenarios. And (very important, this) it's a compelling watch. Narrative drive is created not through a central mystery or problem, but by a long series of small set-ups and pay-offs confronted by the protagonist, one symbol, challenge or character replacing another.
The jumbled mess that spools out is gathered together at the beginning by the idea of 'The Mole' tunneling through the darkness and being blinded by the light: a version of Plato's allegory of the cave in which the form of the good remains inaccessible to humanity. The film is divided into two halves, like the Bible, and the first half is pretty Old Testament. The Mole and a naked boy (Abe and Isaac?) abandon childish things and walk into a violent world full of freaks and gangsters, where eyes are taken for eyes in silent inevitability. You can't rely on anyone in this state of nature, as the boy finds out. The Mole's superpowers keep his new girlfriend Mara alive, but she wants more – the best. The Mole cheats his way through the challenges and surpasses the master gunslingers, heart turning to metal in the process. Meanwhile, Mara's narcissism, rebuffed, turns into masochism, and The Mole is crucified and abandoned.
Like the New Testament, the second half of the film is more boring and easier to parse. Jodo's use of homosexuality / disability / cross-dressing to suggest deviance in the first half may look suspicious, but the mutant villagers in the second I think show that his attitude towards 'the Other' is one of sympathy and delight rather than disgust. Indeed, the romance between the re-born, resurrected El Topo and his new girlfriend is really quite sweet. The decadence of the village looks to me like shots taken at American culture – racism, religious enthusiasm, middle class hypocrisy. El Topo turns into an angel of death at the end ushering in the apocalypse. But rather than reaching an endpoint, the story starts again – its circularity calling attention to its artificiality. Mankind's spiritual yearnings satisfied by tales told over and over again.
Don't know how much of that was in Jodorowsky's head, but the point is: IT DOESN'T MATTER