Six months after the events of The Matrix, Neo and Trinity are now romantically involved. Morpheus receives a message from Captain Niobe of the Logos calling an emergency meeting of all ships of Zion. Zion has confirmed the last transmission of the Osiris: an army of Sentinels is tunneling towards Zion and will reach it within 72 hours. Commander Lock orders all ships to return to Zion to prepare for the onslaught, but Morpheus asks one ship to remain to contact the Oracle. As the Caduceus receives a message from the Oracle, one of the Caduceus crew, Bane, encounters Smith, who reveals that his previous encounter with Neo severed his connection with the Matrix and has made him a rogue program. Smith then takes over Bane’s body and uses the phone line to leave the Matrix into the real world.
In Zion, Morpheus announces the news of the advancing machines to the people. The Nebuchadnezzar leaves Zion and enters the Matrix, where Neo meets the Oracle’s bodyguard Seraph, who leads him to her. After realizing that the Oracle is part of the Matrix, Neo asks how he can trust her; she replies that this is his decision. The Oracle instructs Neo to reach the Source of the Matrix with the help of the Keymaker. As the Oracle departs, Smith appears, telling Neo that after being defeated, he refused to be deleted and is now a rogue program. He demonstrates his ability to clone himself using other inhabitants of the Matrix, including other Agents, as hosts. He then tries to absorb Neo but fails, prompting a battle between Smith’s clones and Neo. Neo manages to defend himself, but is forced to retreat from the increasingly overwhelming numbers.
Neo, Morpheus, and Trinity visit the Merovingian, who is imprisoning the Keymaker. The Merovingian, a rogue program with his own agenda, refuses to let him go. His wife Persephone, seeking revenge on her husband for his infidelity, leads the trio to the Keymaker. Morpheus, Trinity, and the Keymaker flee while Neo holds off the Merovingian’s henchmen. Morpheus and Trinity try to escape with the Keymaker, pursued by several Agents and the Merovingian’s chief henchmen, the Twins. After a long chase, Trinity escapes, Morpheus defeats the Twins, and Neo saves Morpheus and the Keymaker from Agent Johnson.
The crews of the Nebuchadnezzar, Vigilant, and Logos help the Keymaker and Neo reach the Source. The Logos crew must destroy a power plant and the Vigilant crew must disable a back-up power station, to prevent a security system from being triggered, allowing Neo to open the door to the Source. Haunted by a vision of Trinity’s death, Neo asks her to remain on the Nebuchadnezzar.
The Logos succeeds, while the Vigilant is destroyed by a Sentinel, with everyone aboard perishing. Trinity replaces the Vigilant crew and completes their mission. However, Agent Thompson corners her and they fight. As Neo, Morpheus, and the Keymaker try to reach the Source, the Smiths ambush them. The Keymaker unlocks the door to the Source, but the Smiths shoot him dead as he closes the door.
Neo meets a program called the Architect, the creator of the Matrix, who explains that as the One, Neo is himself an intentional part of the design of the Matrix, which is now in its sixth iteration. Neo is meant to stop the Matrix’s fatal system crash that naturally recurs due to the concept of human choice within it. As with the five previous Ones, Neo has a choice: either return to the Source to reboot the Matrix and pick survivors to repopulate the soon-to-be-destroyed Zion, as his predecessors all did, or refuse, causing the Matrix to crash and killing everyone connected to it, which combined with the pending destruction of Zion would mean humanity’s extinction. Neo learns of Trinity’s situation and chooses to save her instead of returning to the Source, to which the Architect responds dismissively.
Trinity is shot as she and Agent Thompson fall off a building. Before she hits the ground, Neo flies down and catches her. He then removes the bullet from her chest. As she starts to flatline Neo reaches into her heart and revives her. They return to the real world, where Sentinels attack them. The Nebuchadnezzar is destroyed, but the crew escape. Neo displays a new ability to disable real-world machines with his thoughts, but falls into a #Topic from the effort. The crew are picked up by another ship, the Hammer. Its captain, Roland, reveals that other ships in defense of Zion were wiped out by the machines after someone prematurely activated an EMP, and that only one survivor was found: the Smith-possessed Bane.