The Matrix Revolutions (2003)
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Neo and Bane lie unconscious in the medical bay of the ship Hammer. Inside the Matrix, Neo is trapped in a subway station named Mobil Ave (an anagram for limbo), a transition zone between the Matrix and the Machine City. He meets a "family" of programs, including a girl named Sati. The "father" tells Neo the subway is controlled by the Trainman, a program loyal to the Merovingian. When Neo tries to board a train with the family, the Trainman refuses and overpowers him.
Seraph contacts Morpheus and Trinity on behalf of the Oracle, who informs them of Neo's confinement. Seraph, Morpheus and Trinity enter Club Hel, where they confront the Merovingian and force him to release Neo. Troubled by visions of the Machine City, Neo visits the Oracle, who reveals that Smith intends to destroy both the Matrix and the real world. She states that "everything that has a beginning has an end," and that the war will conclude. After Neo leaves, a large group of Smiths assimilates Sati and Seraph. The Oracle accepts her assimilation and the Smiths gain her powers of precognition, but it is not clear if she has actually been lost forever in the process.
In the real world, the crews of the Nebuchadnezzar and the Hammer find and reactivate Niobe's ship, the Logos. They interrogate Bane, who says that he has no recollection of the earlier massacre. As the captains plan their defense of Zion, Neo requests a ship to travel to the Machine City. Motivated by her encounter with the Oracle, Niobe offers him the Logos. Neo departs, accompanied by Trinity. Bane, who has stowed away on the Logos, takes Trinity hostage. Neo realizes that Bane has been assimilated by Smith and a fight ensues. Bane burns Neo's eyes with a power cable, permanently blinding him. Neo, discovering an ability to perceive anything part of the machine source code in the real world as wreathed in golden light, sees and kills Bane. Trinity pilots them to the Machine City.
Niobe and Morpheus rush toward Zion in the Hammer to aid the human defenses. Zion's shipyard is overwhelmed by a horde of Sentinels, and the fatally wounded Captain Mifune instructs Kid to open the gate for the Hammer. When it arrives, it discharges its EMP, disabling all the Sentinels present but also Zion's remaining defenses. The humans are forced to retreat and wait for the next attack, thinking it will be their last stand.
Near the Machine City, the Logos is bombarded by thousands of missiles, causing it to crash, fatally wounding Trinity. Neo enters the Machine City and encounters "Deus Ex Machina," the machine leader. Neo warns that Smith plans to conquer both the Matrix and the real world and offers to stop Smith in exchange for peace with Zion. The machine leader agrees, and the Sentinels stop attacking Zion.
The Machines provide a connection for Neo to enter the Matrix. Inside, the Smith with the Oracle's powers steps forth, saying that he has foreseen his victory against Neo. After a protracted battle, Neo realizes there is no other way to win and allows himself to be assimilated. Now connected to the Source, the machine leader sends the deletion signal to the Smith program through Neo's body in the real world. This causes the Neo-Smith clone and all other Smith clones in the Matrix to be destroyed, deleting Smith once and for all. The Sentinels withdraw from Zion, Morpheus and Niobe embrace, and Neo sees a final vision of the machine city while succumbing to his injuries, as his body is carried away by the machines.
The Matrix is rebooted, and the Architect encounters the Oracle in a park. They agree that the peace will last "as long as it can" and that those humans who desire it will be offered the opportunity to leave the Matrix. When questioned about Neo's fate, the Oracle tells Sati that she thinks they will see Neo again as Sati reveals she created a beautiful sunrise over the horizon in Neo's honor. Seraph asks the Oracle if she knew this would happen. She replies that she did not know, but she believed.