The temporary constructs of a feeble human intellect trying desperately to

         justify an existence that is without meaning or purpose. And all of them

               as artificial as the Matrix itself....

The film begins with Neo finding himself trapped in a gateway between th emachine mainframe and the matrix, a gateway which is controlled by the Merovingian. Morpheus, dispirited by the destruction of his ship and the revelation of the prophecy, begins to search for Neo in the matrix, even though Neo is not jacked in. Whilst at this station Neo meets a family of programmes, who tell him that the the station is controlled by a programme called the trainman, who is loyal to the merovingian.

meanwhile Seraph contacts Morpheus on behalf of the oracle and tells him of neo's location. After unsucessfully attempting to get hold of the trainman Morpheus and Trinity confront the merovingian, whom in turn demands the eyes of the oracle in exchange for neo's release. However a standoff ensues and the merovingian is forced to release neo.

Troubled by new visions of the Machine City, Neo decides to visit the Oracle before returning to the real world. She informs him that, as the One, he has a connection with the Source (the Machine mainframe). The Matrix, and the rest of the Machine world, are derived from the Source as well. Thus we learn that all of Neo's abilities - both in and out of the Matrix - exist because of this connection. She characterizes Agent Smith (who is also growing in power) as his exact "opposite", his "negative" and elaborates on the relationship between herself and the Architect. 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 also the Source and eventually the Machine City. later she is assimilated by Smith.

In the real world, the remaining crew of the Nebuchadnezzar and the Mjolnir 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 would have to make a choice to help 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 the ship 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 a severed electric cable. As Bane/Smith appears to have the upper hand he closes in on Neo - only to have his attack thwarted and reversed. Neo can see Smith, the program, in Bane as a fiery form in spite of his blindness. Neo then decapitates Bane/Smith with a lead pipe and releases Trinity, who pilots them towards the Machine City.

It would seem that is the end for Zion as the machine invasion begins - the humans are gradually pushed back as more sentinels attack, yet the return of one of their ships sets of an EMP which disables all sentinels....however the next swarm is already on its way.

Nearing the Machine City, Neo and Trinity are attacked by the city's defence 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, and she dies in Neo's arms.

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 of The Matrix) is beyond the machines' control, and will soon assault the Source to which the Matrix is connected. He offers to help 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 world is now wholly populated by Smiths - the one with the Oracle's powers steps forth, asserting that he has already foreseen his own victory.

One Smith (probably the original) steps forward whilst the other Smiths watch....and a terrific battle ensues between Neo and him. neo eventually relents and allows himself to be assimilated with Smith....however Neo's body suddenly spasms and stiffens as we see a surge of force pass into him from his physical connections (presumably enacting the agreement Neo made with the Deus Ex Machina to destroy Smith). The new Smith's body begins to crack, bright light shining through. This soon passes through to the other Smiths, which begin to explode in a similar fashion.

With the Smiths destroyed, all the programs and humans 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. 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.

The Architect appears and tells the Oracle that she "played a very dangerous game" by attempting to change the way in which the Matrix functioned, to which the Oracle responds, saying that she understood the risk and knew it was worth taking. She asks the Architect what will become of any humans who want to be unplugged from the Matrix, and the Architect replies that "they will be freed". The closing shot of the film depicts a new dawn on the world of the Matrix....

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