Six months after the events of The Matrix 1999, Neo and Trinity now become lovers. An army of Sentinels are tunneling towards Zion and are expected to reach the city within 72 hours. Morpheus's ship Nebuchadnezzar is summoned to Zion to prepare for battle, but Morpheus requests a ship to stay behind to contact the Oracle. This led to an argument between Morpheus and General Lock, who does not believe in prophecies nor Neo.
After his fight with Neo in the previous film, Agent Smith is erased from the Matrix but he manages to hide and has evolved into a sophisticated standalone program, capable of fully cloning just by touching any host - even other Agents. Smith then takes over Bane's body and uses the phone line to leave the Matrix into the real world of Zion City.
In Zion, without the support of General Lock, Morpheus convinces Councillor Hamann (
Anthony Zerbe) to allow the Nebuchadnezzar ship to leave Zion and enter the Matrix to find the Oracle. After realizing that the Oracle is not human but a program of the Matrix, Neo asks how he can trust the Oracle; she replies that it was up to Neo's choice. Oracle advises Neo to go to the Source of the Matrix to find out its essence, with the help of Keymaker.
When the Oracle left, Smith appears he tries to absorb Neo and turn Neo into a clone but is unsuccessful, leading to a battle between Smith and Neo's clones. Neo tries to defend himself, but is forced to retreat in the face of an increasingly overwhelming number of versions of Smith.
Neo, Morpheus, and Trinity go to find The Merovingian (
Lambert Wilson), who is holding Keymaker but is refused. His wife, Persephone (
Monica Bellucci), in seeking revenge against her husband for his infidelity, leads the trio to the Keymaker, in exchange for a kiss from Neo only.
Morpheus, Trinity, and Keymaker flee while Neo stops the Merovingian minions.
Three ships, the Nebuchadnezzar, the Vigilant, and the Logos, are mobilized to help the Keymaker and Neo reach the Source. Team Logos would have to destroy a power plant and Team Vigilant to disable a backup power station, to prevent the security system from being activated, allowing Neo to open the door to the Source. Haunted by visions of Trinity's death, Neo asks her to stay on the Nebuchadnezzar.
Team Logos succeeds, while the Vigilant Ship is destroyed by a Sentinel, killing everyone on board. Trinity decides to enter the Matrix to replace the Vigilant crew and complete their mission. However, she is pursued by Agent Thompson in an unequal fight.
After escaping the pursuit of the clone Smiths, Neo enteres the Source and encounters a program called the Architect, the creator of the Matrix.
The architect explains that as the Chosen One, Neo itself is a purposeful part of the Matrix's design, which is now in its 6th version. Neo was created to prevent system crashes, which recurs naturally since the concept of “human choice” exists in the Matrix.
Like the previous five Chosen Ones, Neo now has a choice. One is to go back to the Source to restart the Matrix and pick survivors to restore the soon-to-be destroyed Zion – that's how his predecessors (5 previous Neo versions) did. The other is to refuse, causing the Matrix to collapse and killing everyone involved with it. Neo learns of Trinity's situation and chooses to save her instead of returning to the Source.
Neo saves Trinity and the two return to the real world, but they are soon attacked by the Sentinels. The Nebuchadnezzar is destroyed, but the crew escapes luckily. Neo displays a new ability to neutralize Sentinals in the real world with his thoughts, but he falls into a coma after casting the power.
The crew is rescued by the Hammer Ship. Captain Roland informs that the other ships protecting Zion were wiped out by the Sentinals after someone prematurely activated the EMP, and only one survivor was found: Smith in Bane's identity.
