Neo's story begins while he is an unknowing prisoner of the Matrix, a digital facsimile of the 20th century world created by a race of sentient machines that control most of humankind. Neo, known within this false world as Thomas Anderson, believes he is working as a software developer by day and works as a computer hacker by night (Neo is his hacker alias). For Anderson, life is ordinary and dull, yet he feels uneasy, as though the world as he knows it is not entirely as it seems.
One day, Neo is contacted by an individual known as Morpheus, supposedly a notorious cyber-terrorist. Morpheus poses the question to Neo: "What is the Matrix?" He reveals to Neo that he can show him what the Matrix is and makes him an offer: to take a blue pill and go back to his ordinary life, or take a red pill and discover the truth. Neo takes the red pill and soon after finds himself ripped away from the world he had always known, waking up naked inside a pod filled with amniotic goo. After this awakening, he is flushed from the pod and discarded in a sewer, only to be retrieved by Morpheus and the crew of the hovercraft Nebuchadnezzar. From then on, Neo's life is altered forever.
Neo is restored to health after his sudden awakening and Morpheus shows him the truth: the world he had been living in was a virtual reality and that the real world was a wasteland ruled by all-powerful machines which had enslaved the human race, turning them all into organic batteries. Eventually, Neo comes to accept the truth, though not without difficulty. Morpheus reveals to Neo that there was a man once born within the Matrix who possessed the power to alter the virtual world as he saw fit, who was responsible for freeing the first pod-born humans and founding the Resistance against the Machines. This individual was known as the One, and after his death, the Oracle prophecized his return and that his coming would bring the destruction of the Matrix and the end of the war. Morpheus is convinced that Neo is the One reborn and takes it upon himself to train Neo in the ways of combat inside the virtual world.
After Neo's training is complete, he is taken to see the Oracle, a rogue program within the Matrix that has been aiding the Resistance against the Machines with her powers of foresight. When he meets with her, Neo is told that he is not the One, that Morpheus was wrong. She also warns that a moment will come when either Neo or Morpheus will die and that Neo will be the one to determine which. The Oracle's prophecy plays out sooner than expected when shortly after the meeting, the Feds intercept the Neb crew and Morpheus is captured.
Neo and Trinity organize a rescue mission and manage to free Morpheus from the clutches of Agent Smith, and during the mission Neo displays abnormal speed and agility that no other redpill is capable of, dodging the bullets of an Agent. After Morpheus is rescued, Neo and Trinity get him out of the Matrix through a phone in the subway, but before Neo can exit he is attacked by Smith. The two engage each other in a heated battle which takes them from the subway, across town and into an apartment block. There, Neo is surrounded by Agents and is seemingly killed by Smith.
Neo does not stay dead, however. In the real world aboard the Nebuchadnezzar (which at that moment is under attack from Sentinels), Trinity sits beside Neo's body and whispers that she loves him. This seems to spur Neo back to life inside the Matrix and he awakens a new man. It is at this moment that Neo's powers as the One awaken and he can see the landscape and citizens of the Matrix in the form of code. Seeing Neo revive, Smith and the Agents try to shoot him dead again, only for Neo to stop the bullets in midair. Smith then rushes at Neo and tries to beat him to death, but Neo effortlessly parries all of Smith's punches and then dives into the Agent's body. Smith is destroyed from within and the other Agents flee, allowing Neo to find an exit from the Matrix. When he wakes aboard the Nebuchadnezzar, Tank activates the ship's EMP wave and disables all of the Sentinels that have boarded the vessel.
An unknown time after the Neb has been saved, Neo sends a message to the Agents within the Matrix, warning them that their control over humanity is not going to last.
The Matrix ReloadedEdit
In the second film, Neo is haunted by nightmares of Trinity's death. These visions come just as the Resistance is put on high alert following news of an army of Machines tunnelling their way through the Earth in order to attack Zion, humanity's last stronghold located near the planet's core. Uncertain of what he should do, he goes to meet with the Oracle once again. The Oracle, in her usual cryptic manner, explains to Neo that there is a task he must fulfill if he is to understand his purpose as the One and save Trinity's life. He needs to find the Source, the very core of the Matrix and the Machines' mainframe, but in order to reach it he will need to find a sentient program called The Keymaker, who is being held prisoner by a power-hungry program called the Merovingian.
Mere moments after the Oracle takes her leave, Neo is approached by his old nemesis Smith, who was supposedly destroyed during their last meeting. Reborn outside the parameters of the system, Smith is now an exile working to his own agenda. More terrifying still, he has evolved into a self-replicating computer virus, capable of imprinting himself upon any of the sentient programs and human inhabitants of the Matrix. Neo finds himself battling against dozens of Smith copies, but he manages to hold his own against them and escapes so that he can meet up with his crewmates.
Later, Neo, Trinity and Morpheus pay a visit to the Merovingian in hopes of negotiating for the Keymaker. The Merovingian feels that the Keymaker is too valuable a prize to give up for anything and dismisses them, but his wife Persephone approaches the Neb crew as they are leaving and offers to help, expressing her disdain for her husband's cruelty. Neo and the others find the Keymaker and after a lengthy chase manage to take him to a safe location. They request that he help them gain access to the Backdoor, a loophole within the Matrix that programs use to travel to and from different locations rapidly. At a building, the crews of the Nebuchadnezzer, Vigilant, and Logos help the Keymaker and Neo reach the Source's door. The crew of the Logos must destroy a nearby power plant in order to prevent a destructive security system from being triggered by the Keymaker's keys, and the crew of the Vigilant must destroy the backup power station. However, the Vigilant's mission goes horribly wrong when a Sentinel throws a bomb at their ship and all their members, including the ones plugged into the Matrix, instantly die.
Trinity (staying in the Nebuchadnezzer because of Neo's wishes to prevent his vision of her death from coming true), upon seeing this turn of events, decides to blow up the back-up station herself. Although a success, her escape is inhibited by an Agent and a duel occurs. Meanwhile, back in the building where Neo, Morpheus, and the Keymaker attempt to reach the Source, the Smiths invade and try to kill Neo, Morpheus and the Keymaker. The Keymaker manages to unlock the door to the Source but is shot by the Smiths and dies.
Neo enters the Source and meets a bearded man in a suit, the Architect, the creator of the Matrix. The Architect reveals there have been multiple versions of the Matrix and with it, multiple versions of the One. The One is a computer anomaly chosen by the Matrix to be used as tool of control. The prophecy is that the One must reach the Source in order to destroy the Matrix and free humanity. However, the One's actual purpose is to return to the Source and choose 16 females and 7 males to rebuild Zion after its battle, which in turn repopulates the city, providing a collection point for the humans who reject the Matrix, making these humans easier to control and less of a danger to the stability of the captive population of pod-bound humans.
After a long conversation, the Architect gives Neo a choice of two exits from the room - one way will lead to the rebuilding of Zion, the other to Trinity's rescue. Neo explodes out of the building in an attempt to save Trinity from death as it was played out in his dreams. Trinity is shot by an Agent as she falls and is caught by Neo just before she hits the ground. Refusing to accept her impending death, Neo removes the bullet lodged in her chest and manages to revive her by starting her heart. In the Nebuchadnezzer, Neo explains his findings to the crew, revealing the prophecy of the One is fake and that Zion will be destroyed in twenty-four hours.
Sentinels approach and destroy the ship, leaving Morpheus stunned by the revelations. Neo saves his friends from being destroyed by the Sentinels by using a new ability which causes the Machines to instantly shut down, but the exertion causes Neo to suddenly fall unconscious. The crew is picked up by the Hammer. The crew of the Hammer explains the catastrophic failure of the battle against the Machines that took place in the real world. The strategy was to use the ship's EMPs, and stay out of each other's range. However, an EMP went off from the Caduceus before the ships could get into position, thus resulting in multiple ships down, and a "slaughter" with the Machines as the victor. Only one survivor is found aboard the Caduceus: Bane/Smith. The film concludes with Neo lying in a medical room - with the Smith-possessed Bane lying opposite him.
The Matrix RevolutionsEdit
Though his body isn't jacked in, Neo's consciousness is trapped in the virtual world. However, he finds himself in unfamiliar surroundings: a subway platform that seems to circle in on itself, preventing him from leaving. Fortunately, he does not remain trapped for long. After threatening the Merovingian into allowing them access to the train station, Trinity and Morpheus retrieve Neo from the platform and bring him with them back to the Matrix's core network, thereby allowing his allies to reconnect his body to his mind.
Before jacking out, Neo decides to pay the Oracle one last visit. He asks her about how he was able to affect the Machines in the real world and about the Ones that came before him as the Architect said. The Oracle explains what she can and warns Neo that a darkness is gathering on the horizon, threatening to destroy both the Matrix and the real world. Neo immediately knows what the Oracle is referring to: Smith. In his viral state, Smith is rapidly consuming every program and bluepill inside the system and will soon dominate the entire Matrix, but he won't stop there; he will eventually corrupt the Machines and destroy both them and humanity unless Neo stops him.
After awakening aboard the Mjolnir, Neo informs his comrades that he knows what has to be done. He decides to embark on a journey to 01, the Machine City itself, in order to try and broker a peace with the Machines and bring an end to the war. Captain Niobe allows Neo to take her ship - the Logos - to Machine territory while the rest of them head back to Zion to assist with defending the city from its imminent attack. Trinity decides to go with Neo to 01 and so they disembark together after saying their goodbyes to Morpheus and the others.
Not long after the Logos gets underway, the ship is sabotaged by Bane who had awoken shortly after Neo had and stowed away aboard the Logos before it took off. Disabling the ship's engines, Bane attracts the attention of Trinity and ambushes her. Neo takes a Lightning rifle and goes to help her, finding Bane holding a scalpel to her throat. Bane commands Neo to drop his weapon and kick it to him and then throws Trinity aside and locks her in the fuse room. As he holds Neo at gunpoint, he taunts him in a distinctly malevolent manner, referring to him by his former Matrix name Mr. Anderson. Neo comes to the chilling realization that Smith is now capable of gaining a presence outside the Matrix and has possessed Bane.
Trinity, locked inside the fuse room, removes another fuse and cuts the lights outside. Neo seizes the moment and lunges at Bane/Smith, trying to wrestle the weapon from him and causing it to discharge. Bane loses his grip on the lightning gun but grabs an exposed power conduit, shoving it into Neo's face and burning his eyes out. Though he has lost his eyes, Neo is not entirely blind: his connection to the Source allows him to see the Source's code even outside the Matrix and he is able to see Smith in front of him. As Smith attacks him with a pipe, Neo parries the blows and wrests the pipe from him before crippling him. Neo then brings the pipe across Smith's head and kills him, watching his code dissipate into blackness now that his host body is deceased. As Smith said before Neo struck him, it was not yet over. Smith was still running rampant in the Matrix and it was up to Neo to put an end to it.
Hours later, the Logos - with Trinity at the controls - approached 01. Neo's Source-vision allowed him to see dazzling pillars of golden light in the distance which only grew brighter as they drew closer. Trinity piloted the ship towards the Machine city, but the city was heavily protected and the ship was carrying no ammunition. Neo was able to cause many attacking Machines to self-destruct, but there were far too many for him to focus on. He urged Trinity to take the Logos up through the sky so that they could come down right on top of the city proper. This maneuver was successful, but Trinity was fatally wounded when the ship crashed, much to Neo's anguish.
Neo exited the wrecked ship and stepped cautiously into 01. Inside, he encountered the Deus Ex Machina, a Machine representative. Neo made his case to the Machines, telling them that Smith was out of control and that he was the only one who could stop him. The Machines were hesitant to trust Neo, but they knew it was only a matter of time before Smith took control of 01 itself. Neo pleaded for peace between the Machines and humanity in exchange for defeating Smith and promised that he would not fail, and so he was jacked into the Matrix for the last time.
Neo entered the cityscape of the Matrix to find that Smith had assimilated everyone within. All of Smith's copies had assembled to watch as Neo fought against a single Smith: the one that had possessed the Oracle. Having assimilated the Oracle and everyone else in the Matrix, Smith's power now equalled that of the One and the two adversaries fought a heated battle using powers that no redpill or even Agent was capable of. Smith seemed to have the upper hand as he beat Neo into submission and smashed him into the road, creating a large crater in the middle of the street. No matter how badly Neo got pummeled, it seemed, he would not give up. Smith seemed genuinely perplexed by Neo's resolve as he had foreseen that he would defeat Neo thanks to the foresight he gained from the Oracle.
As Smith is about to finish Neo, he utters the phrase "Everything that has a beginning has an end, Neo." What Smith does not realize, but Neo does, is that the Oracle is speaking to Neo through Smith. This leads to Neo understanding that to balance the equation, neither of them can exist and thus he allows Smith to duplicate himself through Neo's chest. Smith asks the Neo/Smith clone "Is it over?" The new Smith clone nods confidently. Suddenly, the clone's eyes begin to shine with a bright white light and explode. Moments later, the same thing happens to all of the Smith copies and so Smith and Neo are erased together. Without Smith, the Machines are able to reboot the Matrix, building it anew. They appear to live up to their end of the bargain with Neo as the Sentinels within Zion all leave.