How does Neo realize he is the One? 

Neo begins The Matrix trilogy as Thomas Anderson, a jaded hacker searching for answers about the nature of reality. He’s numbed by the mundanity of his everyday existence and believes there must be something more out there—a belief confirmed when Morpheus enters his life. Morpheus believes that Neo is the One, a prophesied savior who will free humanity from the Matrix, but Neo doubts himself at a fundamental level. The Oracle deliberately misleads him by telling Neo that he is waiting for something—perhaps another life—before he will truly believe enough to be the One. His turning point comes when he enters the Matrix to rescue Morpheus. After Agent Smith kills Neo, he seemingly dies, but Trinity’s kiss revives him. When he stands up, he sees the Matrix for what it is; code that he can manipulate at will. Everything that Morpheus told him suddenly starts to make sense. He’s able to change the world around him, because after his resurrection, miracles are merely math. Because of this new understanding, he’s suddenly able to stop bullets in midair, to take on Smith effortlessly, and to eventually destroy him from the inside at the end of The Matrix Revolutions

Why does Agent Smith return in The Matrix: Reloaded

Neo destroys Agent Smith at the end of The Matrix, but this does not remove the hatchet-jawed special agent from the system. Instead, it frees Smith from the control of the machines who run the Matrix. Smith is “infected” when Neo fights him, as if Neo has given him a virus that reprograms his system. When he’s no longer bound by the laws of the Matrix, Smith becomes an endlessly powerful rogue program. He’s able to reproduce himself endlessly, “infecting” other Matrix residents to make them copies of himself. When he does this, he is literally overwriting the code of the Matrix that makes up other programs, with the objective of filling the Matrix with only copies of himself. He no longer serves the system—having had a taste of power and individual autonomy, he wants to take it over. When Smith encounters Neo again, he terrifies the human rebel by revealing that he also now exists outside of the rules. He has returned to turn the entire universe into himself; if Neo is the One, Smith is the anti-One. 

Why does Neo go to Machine City in The Matrix: Revolutions?

By the end of The Matrix: Revolutions, Neo and the machine overlords of the Matrix realize that Agent Smith has become a danger to both humans and machines. The Oracle warns him that Smith is taking over the Matrix, absorbing everything in his path too quickly to be stopped. Despite all odds and over a century of bitter enmity, Neo—and by proxy the humans of Zion—and the machines find themselves on the same side, united by a common enemy. Meanwhile, outside the Matrix in the real world, the war reaches its peak as the machines attack Zion. Instead of continuing the fight or intervening to save Zion directly, Neo flies to Machine City to confront the leader of the machines. He offers a deal: if they allow him to enter the Matrix one last time, he will stop Smith and free the humans and machines from his tyranny The machines agree and help Neo to “plug in” to the Matrix so he can face Smith in their final battle. Knowing he cannot defeat Smith by force, Neo lets Smith assimilate him, allowing the machines to erase them both and end the war. 

Why does Trinity die in The Matrix: Revolutions

Trinity dies after crashing Niobe’s ship, the Logos, into Machine City. During the approach, Sentinels attack the ship, forcing her to navigate through the semidarkness of its dangerous defenses. She barely manages to land the ship, and as she does, she’s impaled by several thick metal rods. As she lies dying, she tells Neo she is grateful for the time they had together. Neo is distraught, but there’s nothing he can do in the real world to save her. Trinity’s death serves a greater narrative purpose; it reminds the audience that Neo is not all-powerful. It also reminds him that he must face the final battle against either Smith or the machines alone. While Trinity’s love helped Neo believe in himself before—and even saved his life—when she’s gone, he has no option but to act for the greater good. Trinity’s death also reveals the cost of the human-machine war for the human side. Even though Neo succeeds in stopping Smith and ending the conflict, he loses the person he loved most. By the end of The Matrix: Revolutions, it’s clear there is no gain without enormous cost for anyone in the trilogy. 

Why doesn’t Neo destroy the Matrix in the end? 

After Neo defeats Smith, the machines remove Smith’s influence from the Matrix and restore order. Instead of shutting it down, they agree to allow people to leave voluntarily. The Oracle suggests that the Architect—the being who designed the Matrix—will keep his word, allowing the humans still inside to escape. The machines have no reason to continue to kill humans outside of the Matrix if they do not pose a threat in the real world.  The war, as it turns out, was never about keeping the Matrix intact—it was about stopping Zion from disrupting the system. Now that peace between humans and machines exists, the machines have no need to maintain control through violence.  They still need humans to power their energy farms, but the final scene hints that a great deal of humanity will choose to remain inside the Matrix.