Neo (Keanu Reeves) and Bane (Ian Bliss) lie unconscious in the medical bay of the ship Hammer. Meanwhile, Neo finds his digital self trapped in a virtual subway station named "Mobil Ave.", a transition zone between the Matrix and the Machine City. In that subway station, he meets a family of programs, including a girl named Sati (Tanveer K. Atwal), whose father tells Neo the subway is controlled by the Trainman (Bruce Spence), an exiled program loyal to the Merovingian (Lambert Wilson). When Neo tries to board a train with the family, the Trainman refuses and overpowers him.Seraph (Collin Chou) 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 (Hugo Weaving) 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, Seraph and the unresisting Oracle, gaining her powers of precognition.In the real world, the crew 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 (Jada Pinkett Smith) 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. Bane cauterizes Neo's eyes with a power cable, blinding him; however, Neo discovers an ability to perceive the world as golden light. Neo kills Bane, and Trinity pilots them to the Machine City.Niobe and Morpheus set out for Zion with the Hammer to aid the human defenses against the Sentinels. In Zion, the fatally wounded Captain Mifune (Nathaniel Lees) instructs Kid (Clayton Watson) to open the gate for the Hammer. When it arrives, it discharges its EMP, disabling the Sentinels but also the remaining defenses. The humans are forced to retreat and wait for the next attack, thinking that it will be their last stand. Near the Machine City, Neo and Trinity are greeted by thousands of missiles which Neo attempts to destroy, but is overwhelmed by their numbers. The Logos is attacked by the Sentinels forcing them to fly above the missiles for a few seconds. They breach the cloud layer and see Earth's real sky, to which Trinity whispers the word "Beautiful". Upon descent, they lose control causing them to crash the Logos into the Machine City. The crash kills Trinity. Neo enters the Machine City and encounters "Deus Ex Machina", the machine leader. Neo, warning that Smith plans to conquer both the Matrix and will soon conquer the Machine City, 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, Neo finds that Smith has assimilated all its inhabitants. The Smith with the Oracle's powers steps forth, saying that he has foreseen his victory against Neo. After a protracted battle, Neo is weakened and Smith recognizes this as his moment of success. Smith repeats the Oracle's message to Neo, "Everything that has a beginning has an end, Neo", Smith immediately becomes confused and senses something wrong (throughout all three movies up to this point Smith has only addressed Neo as "Mr Anderson"). Neo hearing the words realizes he cannot defeat Smith by fighting and allows himself to be assimilated. An energy surge causes the Neo-Smith clone and all other Smith clones in the Matrix to be destroyed and revert to their previous forms; the Smith clone that fought Neo transforms back into the Oracle. The Sentinels withdraw from Zion, Morpheus and Niobe embrace, and Neo is carried away by the machines. The Matrix reboots, and the Architect encounters the Oracle in a park. They agree that the peace will last "as long as it can", and that all humans will be offered the opportunity to leave the Matrix. The Oracle tells Sati that she thinks they will see Neo again. Seraph asks the Oracle if she knew this would happen; she replies that she did not know, but that she believed.
Output: Question: Who does Neo kill?, Answer: Bane