Six months after the events of the first movie, Captain Niobe (Jada Pinkett Smith) of the Logos calls an emergency meeting of all Zion's Hovercraft Ship Fleet. She has successfully recovered the information left by Captain Thaddeus (in the Animatrix short film "Final Flight of the Osiris," recovered in the video game Enter The Matrix): 250,000 Sentinels are tunneling towards the underground city of Zion and will reach it in 72 hours. Commander Locke, the ranking military officer of Zion, orders all ships and their crews, including Neo, Trinity, and Morpheus, to return to Zion to prepare for the onslaught of the machines. The Caduceus receives a message from the Oracle, and the Nebuchadnezzar, in defiance of Locke's order, ventures out to allow Neo to contact her. Meanwhile, one of the Caduceus' crew members, Bane, encounters Agent Smith, who takes over Bane's body. Bane/Smith then leaves the Matrix via the hard line.
Before the meeting, Neo and Trinity make love, but Neo is having trouble sleeping and has recurring dreams about Trinity falling and being shot by an Agent. After the meeting, he enters the Matrix to meet with the Oracle. Upon arriving, he encounters and spars with Seraph, the Oracle's bodyguard. Seraph is convinced that Neo is who he claims to be, and opens a back door, leading Neo to an isolated courtyard, where he meets with the Oracle. They have a conversation where the Oracle confirms that she is not human, and indeed a program of the Machine World. She also explains that self-aware programs exist in the Matrix besides the Agents that do not function properly, called Exiles. Finally, she says that to reach the Source, effectively the center of the Matrix, Neo needs the assistance of the Keymaker, another rogue program. He can access "back doors" such as the one Seraph used to take Neo to the Oracle. He is held captive by the Merovingian, a powerful and dangerous Exile.
The Oracle wishes Neo good luck and exits the courtyard just before Agent Smith arrives. Smith demonstrates his ability to infect other residents of the Matrix with his program, turning them into copies of himself. He attempts to compromise Neo, and the encounter soon becomes a fight between Neo and hundreds of Smith clones. After an extended, one-sided fight, Neo abandons the battle by flying away, something Smith apparently can't do.
Neo, Trinity, and Morpheus visit the Merovingian, who exists in the Matrix mainly for his own enjoyment; he is accompanied by his wife Persephone and a veritable army of skilled bodyguards. When the protagonist trio requests the Keymaker, the Merovingian is not compliant.
Persephone turns on her husband and takes the three to the Keymaker. Morpheus and Trinity flee the scene with him, while Neo remains behind to combat the Merovingian's henchmen, who use medieval weaponry to little effect.
Morpheus and Trinity take their cargo to the freeway, beginning a chaotic conflict between the heroes, the Merovingian's most skilled bodyguards, and agents loyal to the Matrix (therefore, not including Smith). Collateral damage is massive, but Trinity escapes while Morpheus and the Keymaker are saved in the nick of time by Neo.
Shortly afterwards, the Keymaker explains how to reach the Source. Three ships work together to get Neo to his destiny. The team responsible for taking down the power grid fails when their real-world selves are killed by Sentinels. With the power up, Neo will be unable to reach the source without triggering a fatal alarm system. Therefore, Trinity, against Neo's wishes, perilously enters the Matrix to take down the power.
The Keymaker leads Morpheus and Neo to the necessary door, where they are confronted by the Smith army. The keymaker opens the door safely thanks to Trinity, but dies holding the door for Neo and Morpheus. Neo walks through the final door while Morpheus leaves the Matrix.
Confronting the Architect, who describes himself as the creator of the Matrix, Neo asks the main question: "Why am I here?". The Architect says Neo is "the eventuality of an anomaly" he has been trying to eradicate from the Matrix program. Neo responds by saying the Architect has failed to answer his question, to which the Architect agrees with a slight smile in recognition that Neo was "quicker than the others". Neo is caught off-guard by what he is hearing, but the Architect continues, saying that "the Matrix is older than you know".
The Architect tells Neo there have been many versions of the Matrix, and many predecessors to Neo himself. The wall of monitors surrounding the Architect's room shows possible reactions Neo has to the Architect's revelations. In the course of the dialog Neo realizes "Choice. The problem is choice." The Architect proceeds to detail the history of the Matrix and just how this problem of choice affected its design.
After some modifications about 99.99% of the pod-born humans accepted the program, bringing stability to the Matrix. Neo concludes that the point-zero-one percent who refused the program (and their offspring) constitute the population of Zion. It now becomes clear that the prophecy about "the end of the war" was designed merely as a measure to control both the Zionite rebels and The One.
The Architect continues to reveal that Neo's final task will be to "select from the Matrix 23 individuals – sixteen females, seven males – to rebuild Zion." The Architect then warns Neo "Failure to comply with this process will result in a cataclysmic system crash, killing everyone connected to the Matrix which, coupled with the extermination of Zion will ultimately result in the extinction of the entire human race." Neo tries to call the Architect's bluff saying that humans are necessary for machines to survive, but the Architect merely rebuts the claim, saying that machines are prepared to accept "certain levels of survival" and re-states Neo's dilemma, whether he is or is not ready to accept the responsibility for the death of every human being in this world. As a side-note, he adds that Trinity entered the Matrix to save Neo's life at the expense of her own, and shows Trinity being attacked by an Agent just as Neo had seen in his dream. Despite all logical reasoning, Neo chooses to try to save Trinity over the rest of humanity, and for the first time every screen shows the same decision: Neo walking to the door leading back to the Matrix. After warning the Architect that they had better not meet again (the Architect assures him that they will not), Neo reciprocates Trinity's saving of his life in the first film and uses his powers to remove the bullet and restart her heart.
Morpheus is dismayed when he hears that the Prophecy has been unfulfilled. Neo tells Morpheus that the Prophecy was just a lie and "another system of control." Morpheus refuses to believe it and, echoing the words of his mentor in the first film, Neo says "I know it isn't easy to hear, but I swear to you it's the truth."
The Nebuchadnezzar comes under attack by Sentinels outside the range of their EMP and the crew must abandon ship. As the ship goes down, Morpheus references the story of Nebuchadnezzar from the Bible: "I have dreamed a dream, but now that dream is gone from me" (Daniel 2:3&5). Neo then drops the Sentinels to the ground via a bio EMP (showing for the first time his super-powers in real life, outside the program) and immediately loses consciousness. Morpheus and Trinity proceed to pick up the unconscious Neo and return to Zion. The Hammer then rescues them and brings them aboard. The crew of the Hammer talk to Morpheus and Link, explaining they are the last remnants of a counter-attack organized by Lock in an effort to try driving back the machines in order to buy more time. However, an EMP was detonated, crippling most of the ships in the attack, and the Sentinels slaughtered them in their vulnerable state. Following the battle, the Hammer made a sweep of the battlefield and found a single survivor: Bane. This "chapter" ends with the revelation of Neo laying unconscious on the Hammer next to the now "human" Agent Smith, who has taken control of Bane in order to Kill Neo. The story is concluded in the last film of the trilogy, The Matrix Revolutions
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