Cast
The film's events immediately follow those of The Matrix Reloaded and assume familiarity with the story of the last two films.
The revelation has been made that the prophecy (Neo will set humanity free) was simply another 'system of control' designed by the machines. With Neo having rejected the system of recycling the systematic errors of the Matrix program (Neo's intended function), Agent Smith is left free to destroy the Matrix and soon the Source/Machine City itself, while the pending invasion of Zion means that all life - both human and machine - is facing extinction.
Having no more 'use/purpose' as it were, Neo must now grapple with what he can do to change things not as a messiah, but as a man.
Bane and Neo are both comatose. Morpheus is now depressed and dispirited after the destruction of the Nebuchadnezzar and after discovering the true nature of the Prophecy at the end of the last film. He starts a search for Neo, who he believes could be present in the Matrix while not being "jacked in". Neo is in fact trapped in limbo: a subway station named "Mobil Avenue" that is a transition zone between the Matrix and the Source. At the station, Neo meets a 'family' of programs, who tell him that Mobil Avenue is controlled by the Trainman, a program who is in turn loyal only to the Merovingian.
Seraph contacts Morpheus on behalf of the Oracle, now resident in a different "shell" (in reality, actress Gloria Foster, who played the Oracle in the first two films, died before the completion of the third and was replaced by actress Mary Alice). The Oracle informs Morpheus and Trinity of Neo's captivity. Seraph, Morpheus and Trinity pursue the Trainman, but he evades them. The trio enters Club Hel to confront the Merovingian in an effort to secure Neo's release. After the Merovingian demands "the eyes of the Oracle" in exchange for Neo's release, Trinity provokes a Mexican standoff, forcing the Merovingian to release Neo.
Troubled by new visions of the Machine City, Neo decides to visit the Oracle before returning to the real world. As he enters the Oracle expresses that she had hoped that the batch of cookies that she was baking had been finished before Neo arrived, perhaps a hint that with her metamorphosis she can no longer predict the future as easily. She informs him that as the One, his abilities are actually rooted in a connection with the Source, and because the Matrix is derived from the Source, he has power outside the Matrix too. This is how Neo was able to stop the machines attacking his ship in Matrix Reloaded. She characterizes Agent Smith, also growing in power, as his exact opposite, his negative and elaborates on the relationship between herself and the Architect (Tellingly, each of them ejects an exasperated "Please!" when Neo asks them about the other). She also tells Neo cryptically that "everything that has a beginning has an end", and warns that Smith's power threatens not only the Matrix but the Source, and eventually the Machine City. The Oracle states that the war is about to end "one way or the other".
Zion defends itself from the machine invasion.After Neo takes leave of the Oracle, an army of Smiths arrive, who successfully assimilates the unresisting Oracle, giving Smith her powers of precognition.
In the real world, meanwhile, the remaining crew of the Nebuchadnezzar and the Mjolnir (referred to by the characters as "the Hammer") encounter Niobe's ship, the Logos, and its crew. They successfully reactivate the deactivated ship and begin to interrogate the now awakened Bane, who claims he has no memory of the events of the earlier battle.
After contemplating his visions, Neo announces that he needs a ship to travel to the Machine City, although he cannot explain why at the moment. Roland, the Mjolnir's captain, refuses him, but Niobe who was told by the oracle that she'd have to make a choice helping Neo or not, lets him take the Logos. Trinity decides to accompany Neo.
The two remaining crews plan to return to Zion and avoid the Sentinel army by piloting the Mjolnir through a series of service tunnels through which it is nearly impossible to navigate. Shortly after departing, the Mjolnir's crew discover that Bane has murdered a crewmember and has hidden aboard the Logos, but they are unable to return to warn Trinity and Neo.
Before Neo and Trinity can depart, Bane ambushes Trinity and takes her hostage. Neo fights with Bane, who reveals himself as a manifestation of Agent Smith. During the struggle, Bane/Smith blinds Neo by cauterizing his eyes with high voltage electrical wires. As Bane/Smith appears to have the upper hand he closes in on Neo - only to have his attack thwarted and reversed. In spite of his injury, Neo can see Smith - his connection with the Source manifesting in his recognition of Smith's program inside of Bane. Neo then kills Bane/Smith and releases Trinity, who pilots them towards the Machine City (presumably 01 described in The Second Renaissance).
In Zion, the defenders deploy infantry armed with rocket launchers and Armored Personnel Units in order to protect the dock from assault. The dock is invaded by a massive horde of Sentinels, as well as two giant drilling machines. Meanwhile, the Mjolnir speeds toward Zion, pursued by a large number of sentinels. Just as the remaining humans are about to be overwhelmed, the Mjolnir arrives at Zion and breaks through the gates, setting off an EMP and disabling all electronic equipment in the area. While this finishes off the Sentinels, it also disables the remainder of Zion's defenses. The humans are forced to fall back to the temple entrance and wait for the next swarm that will almost certainly kill them all.
Nearing the Machine City, Neo and Trinity are attacked by the city's defense system, hurling massive numbers of mobile bombs and Sentinels at the Logos. Neo uses his powers to destroy the incoming bombs, but the Sentinels are too numerous. To evade them, Trinity flies the ship above the permanent electrical storm/cloud cover, disabling the Sentinels but also the Logos' engines. After a brief glimpse of sunlight, the ship plunges into a spire of the Machine City. The impact of the collision fatally wounds Trinity.
Neo prepares to confront Smith.Neo emerges into the Machine City to strike a bargain with the machines, personified by the Deus Ex Machina. Neo warns the machines that Smith (who has by now assimilated almost all major parts of The Matrix) is beyond the machines' control, and will soon assault the Source to which the Matrix is connected. He offers to stop Smith in exchange for a ceasefire on Zion. The second wave of Sentinels attacking Zion instantly responds by standing down while the Machines provide a connection for Neo to jack into the Matrix and confront Smith.
The city's population of Smiths stands by and watches while Neo and Smith square off. Smith explains that, possessing the Oracle's foresight, he already knows the outcome of the battle and is certain of Neo's defeat. After an extended fight scene, a defeated Neo allows Smith to assimilate him, but not before repeating Smith's favorite refrain to him: "It was inevitable." By assimilating Neo, however, Smith himself is destroyed. (For main theories as to how and why Smith is defeated, please see the Interpretations section.)
The Smiths are deleted, all programs that have been possessed by Smith return to normal, including the Oracle. The Sentinels that were about to attack the humans withdraw from Zion; the human resistance cheers in victory, while Niobe and Morpheus share a moment of intimate happiness together. Neo, having sacrificed himself to save both the Machines and humans, is unplugged from the Matrix, and his body is respectfully carried away by the Machines.
Smith emerges victorious.The Architect then appears and tells the Oracle that it was dangerous of her to play the system at its own game. The Oracle responds by saying that she has done it for the sake of change, and asks the Architect what will now become of any humans who want to be unplugged from the Matrix. The Architect replies that they shall be freed as such. The Prophecy is finally fulfilled; the human race is finally free as the war between humans and machines is over, and the Matrix is 'destroyed' (its existence for the purpose of enslaving humanity is no more). The closing shot of the film depicts a new dawn on the world of the Matrix, signifying a new beginning (if you notice throughout all three films, every shot of a scene inside the Matrix has a bit of green tinting, symbolizing that it is in a computer program; but in this last scene, that green tint is gone).
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