To start, I know the director has said it’s a metaphor for trans issues and gender identity. This is just a fun exercise in finding similarities. Not an attempt to discount or diminish trans representation.

Gnosticism, specifically Christian Gnosticism, is an esoteric neoplatonist religion and philosophy which emerged in early catholic sects but were ostracized for heresy. They believe that the material world was created by the demiurge, a malicious being who seeks only to be worshipped and appeased by its creations. The true and good God is Sophia, the divine source of wisdom and truth. They believe Jesus Christ was created through Sophia to show humanity the true nature of existence and provide them a way to reach the divine plane of existence, what they call the abstract or Monad. (This is extremely simplified. If there are any gnostics reading this please don’t get mad at me)

Already the parallels to the matrix are obvious. We can see the Agents and the architect as the demiurge. They not only created the matrix but actively try to prevent people from leaving. Morpheus is our Sophia. Though the analogy is not 1 to 1, Morpheus guides neo, our Christ-figure, to enlightenment. Neo is of the matrix, literally made from it. Just as Christ was made from the universe. Hell, the city of the enlightened is literally called “Zion.” The explanation for how Jesus (and others) is able to perform miracles is because he recognizes that the material world is just a lower level of the monad, which he is from. Similarly neo is famously able to bend the spoon by realizing the true nature of his world.