Beginning where the Matrix Reloaded ends, Neo (Keanu Reeves) and Bane (Ian Bliss) are lying unconscious in the med bay of the Hammer. In the Matrix, Neo is trapped in a subway station which is a transition zone between the Matrix and the real world. He meets a family of programs, including a girl named Sati (Tanveer K. Atwal), whose father tells Neo the subway is controlled by the Trainman (Bruce Spence), a program loyal to the Merovingian (Lambert Wilson), who will not let Neo board a train.
Seraph (Colin Chou) contacts Morpheus (Laurence Fishburne) and Trinity (Carrie-Anne Moss) on orders from the Oracle (Mary Alice), who tells them of Neo’s confinement. Seraph, Morpheus, and Trinity enter Club Hel, where they force the Merovingian to release Neo. He visits the oracle, who reveals that Smith (Hugo Weaving) intends to destroy both the Matrix and the real world. After Neo leaves, Smith assimilates Sati and Seraph and the Oracle, which gives him powers of precognition.
In the real world, the crews of the Nebuchadnezzar and the Hammer reactivate the Logos, Niobe’s (Jada Pinkett-Smith) ship. They interrogate Bane, who claims no recognition of the massacre. The captains plan their defense of Zion and Neo requests a ship to visit the machine city. Niobe offers him the Logos. Neo leaves with Trinity. Bane, who has stowed away, takes Trinity hostage. Neo realizes that Bane is assimilated by Smith and a fight begins, in which Bane burns out Neo’s eyes. But he can still sense machine source code and kills Bane. Trinity pilots them to the machine city.
Niobe and Morpheus head for Zion in the Hammer to help in its defense. Zion’s shipyard is overwhelmed by Sentinels. When the Hammer arrives, it discharges an EMP, disabling all the Sentinels along with Zion’s defenses. The humans retreat and wait for their last stand. Outside of machine city, the Logos is attacked by a wave of machines. The ship crashes into a building, fatally wounding Trinity. Neo enters the machine city and encounters their leadership, the Deus ex Machina. He warns that Smith intends to conquer both the Matrix and the real world and Neo offers to stop Smith in exchange for peace with Zion. The machines agree.
They plug Neo into the Matrix, whose population now is all Smiths. With his Oracle powers, Smith forecasts his victory over Neo, who appears to concede defeat and allows himself to be assimilated, but the machines send energy to Smith’s body which destroys all the Smiths. Neo is sacrificed, the Sentinels withdraw, and Morpheus and Niobe embrace. Neo’s body is taken away by the machines, the Matrix is rebooted, and the Architect and the Oracle agree that Neo will return someday.
The movie was written and directed by the Wachowskis at the same time as the Matrix Reloaded and released later in the same year. Critics were disappointed, feeling that the characters took a back seat to the special effects—a pretty common criticism of third movies, as producers always want each movie to be more spectacular than the one before. Nevertheless, it is mind-blowing, particularly the battle for Zion. A fourth film, the Matrix Resurrections, was made in 2021 by Lana Wachowski, which was considered a box-office bomb in a Covid year.
Matrix Reloaded opened at the same time in every major city of the world. Gloria Foster, the Oracle in the previous films, died and was replaced by Mary Alice, who had played her sister on Broadway. It was explained that the Merovingian had punished her by stealing her self-image, so she had to use an old one. Ian Bliss was cast as Bane partly because of his perfect impression of Hugo Weaving. Keanu Reeves was paid $400,000 a minute of screen-time. The crew of the Hammer all had names based on guns: AK (Kalashnikov), Colt, Mauser, and Maggie, short for Magnum. The extras at Club Hel were actual members of the local BDSM scene, who wore their own sado-masochistic gear to save money.