The One, despite his character dying in the finale of 2003’s The Matrix Revolutions.
This was at a time before both Lilly and Lana Wachowski, who directed The Matrix trilogy, underwent gender affirmation procedures in their personal lives.
The original plan was for the character Switch to be a man in the real world and a woman once they entered the Matrix.
Neo himself, Keanu Reeves, was recently asked about this element of The Matrix, to which the actor acknowledged that, while he was not aware of the transgender allegory, he thinks it’s “cool”.