Intrigue

Six months after the events of the first movie, Neo and Trinity are now romantically involved. Neo has nightmares about Trinity attacking a power station inside the matrix and then being pursued by an Agent. Trinity bursts through the window, guns in hand. She turns on her back in mid-air, an agent is pursuing her and jumps after, head first. They exchange gunfire, falling to the streets below in slow motion. Eventually Trinity is shot in the chest.

We see the Nebuchadnezzar from outside as it hovers through the sewers and lands. Inside are Link (Harold Perrineau) and Morpheus (Laurence Fishburne) in the cockpit. Morpheus receives a message from Captain Niobe (Jada Pinkett Smith) of the Logos calling an emergency meeting of all of Zion's hovercraft. 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 (Harry Lennix), the ranking military officer of Zion, orders all ships to return to Zion to prepare for the onslaught. Morpheus states that there is nothing to fear, for he believes the prophecy will come true very soon and end the war. Morpheus asks a ship to remain in order to contact the Oracle, in defiance of Commander Lock's orders. Captain Ballard (Roy Jones Jr.) of the Caduceus volunteers while Nebuchadnezzar returns to Zion to recharge and make repairs.

Morpheus and Trinity are driving to an exit as Morpheus calls Link and asks what happened. Link says a bunch of agents showed up and that suddenly the "coding got all weird." He has never seen anything like it. Morpheus then asks where Neo is now. "He's doing his Superman-thing." The Nebuchadnezzar approaches Zion. Once landed The crew exits the ship and are met by Captain Mifune (Nathaniel Lees) and three A.P.U. escorts. Lock (Harry Lennix) tells Morpheus off for asking a ship to stay behind, when they all had been ordered back to Zion. Morpheus defends himself with his belief that they must have Oracles' advice and that Neo will be the key to ending the war. Lock on the other hand has no confidence in the prophecy and is only concerned with having all the firepower available when the machines reach Zion.

Councilor Hamann (Anthony Zerbe) enters the middle of the discussion. He asks their opinion on what is to be said about the situation to the people at the gathering that evening. Lock believes they should know as little as possible, they wouldn't want to start a panic. Morpheus thinks the truth should be told and that there will be no panic because there is nothing to fear.

Link arrives at his apartment where his girlfriend, Zee (Nona Gaye), is waiting with her sister-in-law, Cas (Gina Torres), her niece (Alima Ashton-Sheibu) and nephew (Joshua Mbakwe). "Uncle Link!" the little ones exclaim as he walks through the door. After welcoming him home, Cas and her kids leave. Zee is not happy at all. Link serving on Morpheus' ship terrifies her. All other ships are home twice as often as Nebucadnezzar. She has also already lost two brothers on that ship and is afraid she will lose him too.

In Zion's temple, Morpheus announces the news of the advancing machines to the people. He confirms the rumors of the machines digging and convinces everyone that there is indeed nothing to be afraid of. While everyone else parties like never before, Neo and Trinity are alone at last and they make passionate love to each other and have the sex of their lives!

The Caduceus receives a message from the Oracle. One of the Caduceus crew, Bane (Ian Bliss), encounters Agent Smith, who takes over Bane's (Hugo Weaving) avatar. Smith then leaves the Matrix through the phone, gaining control of Bane's real body in the real world.

Neo receives a message from the Oracle (Gloria Foster) and the Nebuchadnezzar ventures out so Neo (Keanu Reeves) can contact her. Lock is outraged at Counselor Hamann for giving the Nebuchadnezzar clearance to leave. He did so because he believes their survival depends on more than how many ships they have. Neo meeting her bodyguard, Seraph (Collin Chou). After realizing that Oracle is part of the Matrix, Neo asks how he can trust her. She replies that it is his decision.

Oracle explains that the programs that do their job are invisible, as opposed to those who do not. The latter manifest as what humans refer to as ghosts, vampires etc. "When a program faces deletion, it can either choose to hide out here or return to the Source. Where you must go." "The machine mainframe."

Oracle explains that she is an exiled program and instructs Neo to reach the Source of the Matrix by finding the Keymaker (Randall Duk Kim), a prisoner in the home of the Merovingian (Lambert Wilson). The Keymaker makes keys that can open hidden portals. As Oracle departs, Smith appears, telling Neo that after being defeated, he knew he was supposed to return to the Source to be deleted, but refused, and is now a rogue program. He demonstrates his ability to clone himself using other people in the Matrix, including other agents, as hosts. He then tries to absorb Neo as a host, but fails, prompting a battle between Neo and Smith's clones. Neo manages to hold his own but is forced to retreat from the increasingly overwhelming numbers.

Back in the real-world Neo is unplugged. Neo confirms that he encountered Amith and that he has found a way to copy himself. He also remarks that Smith's attempt to consume him just before the fight felt like he did in the hotel hallway where Smith had shot him six months before.

In Zion the council and all crews are gathered. Lock explains their current situation and tactics. The council have limited confidence in these tactics. They then ask if there has been word from the Nebucadnezzar. The council asks for two volunteer ships to go search for them, against Lock's protests. Captain Soren (Steve Bastoni) stands up immediately. No other reacts to the request. Bane/Smith suggests to Ballard that they should volunteer, but Ballard just tells him to shut up. Eventually Niobe declares her willingness to search for the missing party, to Lock's surprise and horror.

Neo, Morpheus and Trinity (Carrie-Anne Moss) visit the Merovingian and ask for the Keymaker. The Merovingian, a rogue program with his own agenda, refuses to let him go. His wife Persephone (Monica Bellucci), tired of her husband's attitude and seeking revenge on her husband for his infidelity, betrays him and leads the trio to the Keymaker, on the that Neo kiss her as if she were Trinity, she wants to remember what love feels like. Trinity protests by pulling a gun at Persephone, but as they need the Keymaker she has no choice but to back down and look on in anguish.

Persephone allows one of the Merovingian's henchmen to escape to tell her husband. The Merovingian soon arrives and, while Morpheus, Trinity and the Keymaker escape, Neo fights the Merovingian's supernatural servants. Neo eventually kills them all. Disappointed, the Merovingian spits that he has survived Neo's "predecessors" and storms out, shutting the door behind. Neo breaks through the door and finds himself high up in the mountains.

Meanwhile, the Keymaker connects the door at the end of a hallway to a sub-level parking garage, but Morpheus fails to close the door before one of the Twins gets an arm between the door and the door frame. In the meantime, the Keymaker acquires a car, and Trinity runs over and gets in the driver's seat while Morpheus holds the Twins at bay with a Katana he'd taken from the Merovingian's hallway and a pistol. Morpheus gets in the car and they flee. As they drive away one of the twins closes the door in Neo's face.

Morpheus and Trinity are trying to escape with the Keymaker on the highway, facing several Agents and The Twins (Neil and Adrian Rayment). Trinity and the Keymaker obtain a motorcycle from a passing semi-trailer and continue towards their exit. It is not long however before an Agent takes control of another semi-truck, forcing Trinity to turn around. Police follow and are soon transformed into more Agents. Morpheus comes towards them on the roof of another semi-truck and grabs the Keymaker. Trinity is no longer being pursued and escapes, as it is the Keymaker the Agents want this time. Though he puts up a ferocious fight, Morpheus is thrown off, but Niobe catches him on the hood of her car. Morpheus gives Niobe a silent pointing gesture and she races him to a point in front of the semi. Just as the Agent is about to terminate the Exile, Morpheus jumps on him, throwing him off. The Agent is still to relocate to the driver's seat of the same semi-truck, and forces Niobe's car out of traffic. Further back another Agent is in control of another semi-truck and turns the truck, aiming for the other truck and a head-on collision. Ultimately, the Twins are killed, and Neo flies in to save Morpheus and the Keymaker.

Zion's remaining ships prepare to battle the machines. Within the Matrix, the crews of the Nebuchadnezzar, Vigilant and Logos help the Keymaker and Neo reach the door to the Source. The crew of the Logos must destroy a power plant in order to prevent a security system from being triggered by the Keymaker's keys, and the crew of the Vigilant must destroy a back-up power station.

Haunted by a vision of Trinity's death, he asks her to remain on the Nebuchadnezzar. The Logos is successful, but the Vigilant is destroyed by a Sentinel. Trinity replaces the Vigilant crew and completes their mission. Agent Thompson corners her and they fight.

As Neo, Morpheus and the Keymaker reach the Source through a hallway of shortcuts to other doors in the Matrix, the Smiths appear and try to kill them. The Keymaker unlocks the door to the Source, allowing Neo and Morpheus to escape the Smiths, but the Keymaker is killed. Before taking his last "breath," he tells Morpheus which door to take to get home and gives Neo the key he needs to open the special door. Simultaneously an Agent is heading for Trinity without her knowledge. Neo enters the door of light.

He is now in a room where the walls are made up of old-fashioned television screens. Neo meets a program called The Architect (Helmut Bakaitis), the Matrix's creator. In the complex conversation that follows, the Architect explains that Neo is part of the design of the Matrix. There were multiple previous versions of the Matrix and the One, which is now in its sixth iteration.

The Architect describes the first Matrix, which was perfect and therefore failed. The Architect tried again, making it reflect the human nature, but in vain. The problem was discovered by "an intuitive program, initially created to investigate certain aspects of the human psyche." The Oracle discovered that the humans had to be given choice.

Neo is meant to stop the Matrix's fatal system crash that naturally recurs due to humans' free will, leading to dozens of humans gradually refusing to accept the simulation. As with the five previous Ones, Neo has a choice: either reboot the Matrix from the Source and pick 23 survivors to repopulate the soon-to-be-destroyed Zion, as his predecessors all did, or go to save the imperiled Trinity, causing the Matrix to crash and killing everyone in it.

Unless Neo returns to the Source to reboot the Matrix, it will crash, killing everyone connected to it. Combined with Zion's destruction, this would mean mankind's extinction, and the machines would survive on some lesser energy source. He doubts, however, that Neo will accept the extinction of all humans.

The Architect presents Neo with two doors. The one to his right leads to the Source, and the one on the left to Trinity and the downfall of man. The old man can tell that Neo's feelings are blinding him from the "fact" that Trinity will die either way.

Neo learns of Trinity's situation and chooses to save her instead, as Trinity falls out of a window and is shot by the Agent she is fighting. Neo catches Trinity, but she dies. Unwilling to let her go, Neo uses his powers to remove the bullet and restarts her heart.

They return to the real world, where Sentinels attack them. Morpheus fails to understand why the prophecy has not come true. Neo tells him and the others that they have 24 hours to save Zion, and that the prophecy was just another form of control, a lie. Morpheus has major trouble accepting this, but before they can contemplate this complexity, their proximity alert sounds.

The Nebuchadnezzar is destroyed, but the crew escapes. As the Sentinels catch up to them, Neo realizes he can sense the machines in the real world and telepathically destroys them but falls into a coma. The crew are picked up by another ship, the Mjolnir. The Mjolnir's captain reveals that the machines wiped other ships defending Zion after someone prematurely activated an EMP. Only one survivor was found: the Smith-possessed Bane, who lies beside Neo in the medical bay, also unconscious.