Neo (The Matrix) - The Matrix Reloaded

Approximately six months between the events of the first film and The Matrix Reloaded, Neo is now fully confident in his ability to manipulate the artificial world within the Matrix. Not surprisingly, he no longer uses firearms and instead prefers martial arts. Dispensing with the long black trenchcoat and black shirt he wears at the conclusion of The Matrix, Neo now prefers a cassock with a high-rise mandarin collar. He and Trinity are now lovers. Neo seeks more advice from the Oracle, unsure of his purpose, while Zion prepares for a massive attack by the Machines from over 250,000 Sentinels – giant jellyfish-like machines. The Oracle directs him on a quest to find the Keymaker, a personified program that has access to numerous backdoors within the system. The Keymaker will be able to lead Neo safely to the Source, the programming heart of the machine world, which contains the programs sustaining the Matrix.

As the Oracle leaves, Agent Smith (now known simply as Smith) appears, and it is revealed that Neo had separated Smith from the rest of the Matrix code by shattering him, giving him a life independent of the machine's systems, and now the two of them share a "connection" to each other. Smith is no longer an Agent of the Matrix, but has become more virus-like, able to insert his code into other systems and infect other programs and human minds to make copies of himself. Neo fends off hundreds of these Smiths and escapes. Later, he, Morpheus, and Trinity steal the Keymaker from his keeper, The Merovingian. During this time, Neo stays behind to fight off the Merovingian's men and becomes separated from the others. He flies off to help them and only arrives in time to save Morpheus and the Keymaker from two agents crashing two semis together.

The Keymaker explains that two power stations elsewhere in the Matrix must be disabled in a short time window to successfully disable the security system of a building where the door to the Source will appear, allowing Neo to reach it. This task is accomplished; but the Keymaker is killed, a hovercraft is destroyed, and Trinity is put in jeopardy by Agents of the Matrix; a vision that Neo has seen earlier in his dreams. Entering the door, Neo finds himself confronted by the Architect, a program which created and designed The Matrix.

The Architect presents Neo with a radically different explanation of his origins and purpose, claiming that Neo is actually the sixth "One". He goes on to say that Zion has been destroyed by the machines five times before; faced with the dilemma of allowing humanity to be destroyed, or allowing the machines' preferred status quo to be reconstructed, Neo's five predecessors have helped reload, or restart the Matrix, before being allowed to rebuild Zion with a handful of freed humans. The productive output of the Matrix is based upon this repeated cycle of destruction and recreation, to keep the human minds which power it in a stable structure. The Oracle is as much part of that self-perpetuating design as the Architect, Neo is told, and the prophecy of The One is designed to ensure it runs smoothly each time.

The Architect warns of the annihilation of all human life in and out of the Matrix if he did not enter the Source door to reload the Matrix, but unlike his predecessors, Neo does not enter the door to the Source; he chooses not to believe the Architect's dire warnings of consequences, and to save Trinity instead. He saves her, just before she falls to the ground from the top floor of a power plant. However, as she was shot before she fell, she dies of her wounds. It is at this point that Neo displays the ability to heal/resurrect a person, as he reaches into her virtual body and restarts her heart.

Together, they exit the Matrix and return to the real world. Neo tells Morpheus that the Prophecy was merely another system of control, and that Zion's destruction is imminent. A group of Sentinels begin to converge on their hovercraft, so that Neo and the others are forced to abandon it and flee. Neo, realizing that he can now sense the sentinel, stays behind, and is able to deactivate the Sentinels by a hitherto unknown ability, to control objects while outside of the Matrix. The effort of doing so renders him unconscious.

He and the crew are rescued by the hovercraft Mjolnir/Hammer, the crew of which is dealing with a mystery in the form of Bane, a crew member from another ship, who is the only survivor of an ill-fated attack by the Zion fleet. Unbeknownst to anyone, Bane has become caught and infected by Smith.