- The Other Darrin: Mary Alice replaced Gloria Foster as the Oracle, as Foster died shortly before filming began. It's explained In-Universe via The Nth Doctor, with a story about Ramachandra selling her original shell's termination code to the Merovingian in exchange for his daughter's safety.
- Release Date Change: The film was intended to be released weeks after Reloaded. Instead, it was released six months later.
- Torch the Franchise and Run: Due to its Grand Finale status for the Trilogy, the film has Agent Smith, Trinity, and Neo all being dead by the end. However, in 2019, The Matrix Resurrections was confirmed with Lana Wachowski returning to write and direct along with Keanu Reeves and Carrie-Anne Moss confirmed to reprise their roles.
- What Could Have Been: The script and storyboards of the final fight had an addition to the "Superpunch" not present in the final film, involving Neo using his life-force to generate an energy ball to smash Smith with. It was likely removed as it was a bit too far on the mystical side of things.
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