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Reaching the hard line, Morpheus and Trinity return to the real world, but Neo is trapped by Agent Smith. Rather than run, Neo decides to stand his ground and fight Smith. Neo skillfully engages Smith in combat, almost seeming to be Smith's equal. In the end Neo is able to subdue him, trapping him in front of an oncoming train. Smith possesses the body of the driver and emerges from the train. Realizing that he cannot win this fight, Neo runs from the subway station.

On their way back to the phone, which serves as the exit for "redpills" to leave the matrix, the crew of Morpheus' ship are betrayed by . Morpheus is captured and held by Agents within the Matrix. Escaping death at the hands of Cypher, Neo and Trinity learn that the Agents seek to hack into Morpheus's brain, forcing him to tell them the access codes to the Zion mainframe. After refusing to sacrifice Morpheus (to prevent him from leaking the codes), Neo decides to attack the government building. He and Trinity proceed to fight their way to the roof level of the building, where they are confronted by . Neo unloads two entire magazines of ammo on Jones only to have every one of them be dodged effortlessly. When Jones returns fire, Neo proves to be capable of dodging bullets himself, fluidly moving in a way that only Agents were thought to be capable of moving. Jones is then shot by Trinity at point-blank range. Using an armed chopper, Neo and Trinity successfully rescue Morpheus from the floor of the building that he was on. Having just completed a successful rescue mission in a building protected by heavily armed guards and agents, a feat never before achieved, Morpheus takes this as evidence confirming that Neo is indeed The One, dismissing the Oracle's words by saying that she merely told Neo "exactly what you needed to hear". He further elaborates "Neo, soon you're going to realize just as I did, there is a difference between knowing the path, and walking the path" (this phrase is a clear reference, one of the key influences of the film).

After several days aboard the , Neo is taken to meet the , who has the power of foresight within the simulated world. She tells him that he has the "gift", but appeared to be waiting for something "Your next life, maybe. Who knows?", telling him in this life he's not the one. The Oracle warns him that an event will come where he will have to choose between his own life or that of Morpheus, and that one of them will die.

Neo is rescued and his body is healed of the effects of his suffered in the power plant. Once Neo regains consciousness and is able to walk around, Morpheus tells Neo the truth about the Matrix, about the real world, and about the fate of humanity. At first Neo refuses to believe him, but he ultimately embraces the truth. Afterward, Morpheus also tells Neo about the prophecy of The One, and how he believes that Neo is The One. The next day, Neo begins his "training", becoming knowledgeable in many forms of combat by having various training programs uploaded directly into his brain. He also receives further instruction from Morpheus on subjects such as "freeing his mind" from the restrictions of the Matrix and the existence of its Agents.

Neo is offered the choice to remain in his everyday life or to learn what the Matrix is. Accepting, he takes a drug (commonly called the "") designed to disrupt his body's neural connection to the Matrix, and wakes up disoriented and alarmed to find himself weak, hairless, and naked in a pod of liquid, in which he is connected to many wires.

During the years prior to the events of The Matrix, Anderson spent his time trying to find the one man whom he thought could tell him what the Matrix was: a supposed terrorist known only as Morpheus. Anderson is suddenly contacted by Morpheus via a cellphone mailed to his office, but is almost immediately captured by the 's Agents, led by . After refusing to co-operate with the agents, Neo has an electronic bug implanted within his Matrix-simulated body, so that his actions can be tracked and those seeking to make contact from the free world can be traced and destroyed. He is contacted by Trinity, freed from the bug, and taken to meet Morpheus.

At the start of the series, Thomas Anderson is one of billions of humans neurally connected to the Matrix, unaware that the world he lives in is a virtual reality. In his legitimate activities, he is a quiet for the "respectable software company" Metacortex; but he is also a computer who penetrates computer systems illicitly and steals information, under his hacker "Neo". During his time as a hacker, Anderson has learned about something known only as "". It is described by Morpheus as a vague notion that Neo has felt his whole life that "there is something wrong with the world".

The word 'Neo' is an anagram of the word 'one', but also for 'eon'. Neo is also Greek for 'new,' suggesting messianic overtones for his mission in the Matrix. In , eons or are emanations from or aspects of God, one of which was regarded by many Gnostics to taken human form as . The name "Neo" also might be a play on words from the middle posterior lobe of the , also known as the . The neocerebellum receives input from the cerebral cortex and is involved in muscle coordination during movement and in learning skilled motor skills. 

When the nature of the Matrix is revealed to him, Neo becomes part of the human resistance and he is revealed to be 'The One'. The Matrix film trilogy explores his abilities as The One to manipulate his computer-simulated reality to his will, and his messianic mission as the savior of mankind.

The character Neo lives in the world of the Matrix, an illusory construct in which humans are neurally connected to a massive computer system that simulates the world of the late 20th century. This system has been developed by to keep the human population as tools for the machines' survival; the machines use a form of fusion in addition to the bioelectrical energy of human beings as their primary energy source. Previously, the machines had relied upon ; but after the war between humans and machines broke out, humans cut off the machines' energy source by creating an immense, black cloud that blocked out the sunlight. Those who live their entire lives connected to the Matrix are unaware that their reality is not in fact real, nor that there is a human rebellion by the few 'free' humans in the city of . From time to time, individuals are freed from the Matrix, a risky and complex operation. There is a legend or prophecy amongst free humans (which some believe and others scorn) that there was a human who, when connected to the Matrix, could override its computer-simulated rules and perceive and manipulate its code directly. Thus, within the of the Matrix, this person would appear to be able to perform miracles. This person is called in legend "The One". This person supposedly freed the founders of Zion, then died afterwards, but his return was foretold. His or her discovery is the subject of a lifelong quest by , a hovercraft captain of the Zion fleet, who hopes that The One will bring the between Man and Machine to an end.

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