The Matrix films were trans allegories. this isn’t a fan theory either, the the Wachowskis (the two sisters who directed the films) said their original intention for the films was to be a trans allegory. (source)

“That was the original intention but the world wasn’t quite ready,”

Quote by Lilly Wachowski. she and her sister came out as trans after the films came out

Book

Allegory of Jesus’s resurrection.