The Matrix Revolutions begins immediately after the events of the second movie. As a result of his struggle with the Sentinels, Neo returns to consciousness to finding himself caught in an isolated train station-like limbo only accessible by order of the Merovingian, from which his mind is unable to free itself. He remains trapped until freed by Trinity (assisted by Morpheus and Seraph), who threatens the Merovingian in a Mexican standoff unless Neo is freed.
Neo determines, through his new abilities of foresight, that in truth the Oracle's prophecy was correct in that The One was predetermined to return to the Source to stop the war. The Architect, however, altered the prophecy and forced Neo's predecessors to end their path with Zion's destruction and the reloading of the Matrix. After a final visit to the Oracle, Neo learns it is not the approaching Sentinels that he should fear, but Smith, whose clones are multiplying and threaten to destroy both the Matrix and the real world. Building on the Oracle's previous explanations about the nature of choice, Neo learns that the Architect's assertion that his choice to save Trinity would inherently lead to the extinction of humankind was incorrect, due to his nature as a purely mathematical being. Having told Neo that he now has the power to choose to end the war and defeat Smith, the Oracle then states "Everything that has a beginning has an end, Neo". Neo must now go to the heavily-guarded Machine City in hopes of stopping the Sentinels and Smith. But soon after Neo leaves, hundreds of Smiths come and assimilate Seraph, Sati, and the Oracle.
Neo and Trinity are given the Logos, a hovercraft commanded by Morpheus's former lover, Niobe, in what seems to others as a suicidal journey to the Machine City. Meanwhile, Captain Roland and the Nebuchadnezzar's surviving crew of Link and Morpheus in the hovercraft Hammer/Mjolnir return to Zion, which is now besieged and losing to the Machines. Neo and Trinity are ambushed by the stowaway Bane/Smith, who blinds Neo, but is killed when Neo discovers an ability to 'see' programs and Machines independently of his eyesight. Neo, with Trinity as pilot, guide the Logos past the Machine City's defenses, but in the effort the Logos crash-lands, and Trinity sustains fatal injuries and dies.
Neo encounters the Deus Ex Machina, a Machine construct, and offers Smith's destruction in exchange for a truce. The offer is accepted; Neo enters the Matrix to find that the Smith program has copied itself throughout the simulated world, and has turned it into a rainswept dark simulation. One of the copies of Smith, having assimilated the Oracle and obtained as much freedom and control over the virtual world as Neo, faces Neo alone. For a while, the two fight evenly with no real advantage, but ultimately, the tireless Smith begins to wear out Neo and takes control of the fight. Realizing he cannot win with brute force, Neo baits Smith into assimilating him, which allows Neo to destroy all the Smith clones from the inside (much the same way he defeated Smith in the first movie), but it is too much for Neo and he dies.
Neo's body is respectfully taken away by the Machines in the Machine City, while below in Zion, the Machines stop their attack and retire in deference to the peace that Neo bartered. Neo then dies, his primary code being inserted into the Matrix which allows it to reboot.
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Famous quotes containing the word matrix:
“As all historians know, the past is a great darkness, and filled with echoes. Voices may reach us from it; but what they say to us is imbued with the obscurity of the matrix out of which they come; and try as we may, we cannot always decipher them precisely in the clearer light of our day.”
—Margaret Atwood (b. 1939)