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, a transition zone between the Matrix and the machine world. 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 tells him that “everything that has a beginning has an end.” After Neo leaves, a large group of Smiths assimilates Sati and Seraph. The Oracle does not resist assimilation and Smith gains her powers of precognition.
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, blinding him. Neo discovers that he can still “see” machine source code in the real world and uses this ability to kill Bane. Trinity pilots them to the Machine City.