There are levels of survival we are prepared to accept. However, the relevant

        issue is whether or not you are ready to accept the responsibility for the death

             of every human being in this world.

It is six months since the last installment, and Captain Niobe of the Logos Hovercraft ship calls an emergerncy meeting of all Zion's fleet commanders. She has received information that 250,000 sentinels are tunnelling towards the underground city of Zion, and that more alarmingly they wil reach it in 72 hours. Commander locke, the ranking officer, orders all ships and their crews (including Neo, Trinity and Morpheus) to return to Zion and prepare for battle. 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.

Before the meeting, Neo is having trouble sleeping and has repeated dreams about the death of Trinity. 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 beside the Agents that do not function properly, called Exiles. Finally, she says that to reach the Source, effectively the centre 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.

As the oracle leaves the courtyard Agent Smith arrives and demonstrates his ability to take over the bodies of other residents, turning them into copies of himself. The encounter results in neo fighting with hundred's of Smith's before Neo manages to escape.  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 trio requests access to the Keymaker, the Merovingian is not compliant. However 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. Neo then leaves and saves Trinity, Morpheus and the keymaker.

Back in the real world, 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 copies. 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.

Neo then finds himself confronmting the architect, who describes himself as the creator of the matrix. The architect reveals that neo is the eventuality of an anomoly he has been attempting to eradicate from the matrix programme. Even the architect is surprised by Neo's response and tells him that he was 'quicker than the others,' implying th ematrix is older than neo would care to imagine. It would appear that the problem is that of choice, and the architect continues to detail the history of the matrix and how such  problem effects the design.

After some modifications about 99.99% of the pod-born humans accepted the program, thus 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 - 16 females, 7 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 that claim by 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. he shows how Trinity entered the matrix to save Neo at the expense of her own life, and that she was being attacked by one of the agents. Despite logic neo chooses to save Trinity over the rest of humanity, and he saves her life by removing a bullet from her heart.

Morpheus is dismayed when he hears that the Prophecy has been unfulfilled, and struggles to accept that it has all been a lie. meanwhile the Nebuchadnezzar comes under attack by Sentinels outside the range of their EMP and the crew must abandon ship. As the crew stand helplessly Neo manages to stop the sentinels via EMP, before losing consciousness. The crew, with the unconscious Neo, are picked up by another ship, The Logos, and the ship heads back to Zion. The film ends with Neo laying unconscious on the Logos next to the now "human" Agent Smith, who has taken control of Bane.

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