Watch The Matrix Reloaded Online

Six months after the events of the first movie, Neo wakes up after a nightmare where Trinity had been shot by an Agent while falling from a building and begins to plummet to the ground. Morpheus receives a message from captain Niobe (Jada Pinkett Smith) of the Logos calling an emergency meeting of all Zion's hovercraft ship fleet. She has successfully recovered the information left by Captain Thaddeus (in the Animatrix short film "Final Flight of the Osiris," recovered in the video game Enter the Matrix): 250,000 Sentinels are tunneling towards the underground city of Zion and will reach it in 72 hours. Commander Locke, the ranking military officer of Zion, orders all ships and their crews, including Neo, Trinity, Morpheus, and new operator Link, to return to Zion to prepare for the onslaught of the machines. Morpheus asks a ship to remain behind to contact the Oracle, in defiance of Commander Locke's orders. The Caduceus receives a message from the Oracle, and the Nebuchadnezzar, also in defiance of Locke's order, ventures out to allow Neo to contact her. Meanwhile, one of the Caduceus crew members, Bane, encounters Agent Smith, who takes over Bane's body. Bane/Smith then leaves the Matrix via the nearby hard line.

After returning to Zion, the crew of the Nebuchadnezzar attend a meeting in Zion's temple where Morpheus announces the news of the advancing machines to the people, but his positive attitude and stirring speech gives them courage. As a dance breaks out, Neo has recurring nightmares about Trinity being shot by an Agent during a gunfight down the side of a building and falling to her death. Neo receives a message from the Oracle the next morning and he soon meets her and her bodyguard Seraph. Seeing that the Oracle is a part of the system Neo asks how can he trust her if she is just another form of control. She responds by saying that only he can make the choice if she is ally or enemy. The Oracle explains that she is an exiled computer program and instructs Neo to reach the Source, by finding the Keymaker, a prisoner in the home of the Frenchman program the Merovingian. The Keymaker, as his name implies, can make keys that can transport anyone to any where in the world provided there is a door at the other end. As Oracle departs, Agent Smith appears despite his apparent destruction in the first film, although technically he is now just "Smith" without the "Agent" prefix. Missing his earpiece (which he sent to Neo in a package as a sign of his survival), Smith tells Neo that after being defeated by him he knew that he was supposed to return to the Source to be deleted but he refused and now he is no longer bound by rules or a duty to remove threats from the Matrix. Following that line of reasoning, he states that he is "apparently free", but then subsequently asserts that because he no longer has a purpose, he is not actually free. He demonstrates his ability to clone himself using the people of the Matrix as hosts (even assimilating the body of an Agent), prompting a battle between Neo and many clones of Smith. Neo holds his own using his knowledge of martial arts and a large pole but is eventually overwhelmed, covered by a massive pile of Smith's clones. He throws them off and flies away, leaving the Smith clones to disperse.

Neo, Morpheus, and Trinity visit the Merovingian and ask for the Keymaker, but the Frenchman refuses them. His wife, Persephone, tired of her husband's attitude and infidelity, turns against him and leads the trio to the Keymaker. (Her desire to have her husband know of her treachery becomes apparent when she shoots one of his assistants, and then instructs the other to tell the Merovingian what happened, or meet the same fate as his comrade.) While Neo battles the Merovingian's skilled guards, Morpheus, Trinity, and the Keymaker escape onto the nearby freeway with the ghostly Twins, Agents, and the police in pursuit. Morpheus defeats the Twins by destroying their car, and then saves the Keymaker from an Agent. Both are then retrieved by a flying Neo. In the real world, the remaining ships at Zion prepare for a battle with the machines. 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 destroy 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, revealed as the creator of the Matrix. The Architect informs Neo that 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 a tool of control. Because humanity rejected the "perfect" Matrix, the world that has come to be accepted is flawed and remains an unbalanced equation. The One is therefore the sum of the remainder of that flaw. 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 the final battle, which in turn repopulates the city to provide the next round of humans for the "rebellion" and the next iteration of the "Prophecy", a confirmation of Morpheus' statement from the last film about The One who previously freed himself and others. Failure to do so will result, not only in the massacre of Zion's population, but the unresolved Matrix error will result in the death of every human attached to the Matrix, and thus the extinction of the human race. Neo retorts that, since the machines need humans for their power, they will not allow this, but the Architect calmly replies that without the humans, "there are levels of survival we are prepared to accept."

After conversing, 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, and through this, the downfall of humanity. 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 they fall from a building 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 false 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 killed 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 Mjolnir (referred to by the characters as "the Hammer"). The crew of the Mjolnir explains that they were to lead an attack on the army of Sentinels advancing on Zion. The strategy was to use the ship's EMPs, and stay out of each other's range. However, an EMP was detonated by the Caduceus before the ships could get into position; multiple ships were left without power, and the Sentinels emerged victorious, having slaughtered any ship that could not get away. 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 Reloaded was largely filmed at Fox Studios Australia in Australia, concurrently with filming of the sequel Revolutions. The freeway chase scene was filmed at the decommissioned Naval Air Station Alameda in Alameda, California. Producers constructed a 1.5-mile freeway on the old runways just for the movie (Which was later used by the Mythbusters in testing several myths). Portions of the chase were also filmed in Oakland, California, and the tunnel shown briefly is the Webster Tube connecting Oakland and Alameda. Some post-production editing was done in old aircraft hangars on the base as well.

The city of Akron was willing to give full access to Route 59, the stretch of freeway known as the "Innerbelt", for filming of the freeway chase when it was under consideration. However, producers decided against this as "the time to reset all the cars in their start position would take too long". MythBusters would later reuse the Alameda location in order to explore the effects of a head-on collision between two semi trucks.

97% of the materials from the sets of the movie were recycled. For example, tons of wood were sent to Mexico to build low-income housing.

Scenes from the movie Baraka by Ron Fricke were selected to represent the real world shown by the wallmonitors in the Architect's room.

Sound editing on the Matrix Trilogy was completed by Danetracks in West Hollywood, CA.

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