Intrigue

After the events of The Matrix Reloaded, Bane (Ian Bliss) and Neo (Keanu Reeves) are unconscious. Neo's neural patterns suggest he is in the Matrix. Morpheus, dispirited after the destruction of the Nebuchadnezzar and discovering the true nature of the Prophecy, starts a search for Neo within the Matrix despite him not being jacked in.

Neo finds himself trapped in a subway station named Mobil Ave, a transition zone between the Matrix and the machine world. Neo meets a "family" of programs, including a girl named Sati (Tanveer K. Atwal), whose father tells Neo the subway is controlled by The Trainman (Bruce Spence), an exile loyal to the Merovingian (Lambert Wilson). When Neo tries boarding a train with the family, the Trainman refuses to let him aboard and punches Neo into a wall.

Seraph (Collin Chou) contacts Morpheus (Laurence Fishburne) on behalf of the Oracle (Mary Alice). The Oracle informs Morpheus and Trinity (Carrie-Anne Moss) of Neo's confinement. Seraph, Morpheus, and Trinity pursue the Trainman to secure Neo's release, but he escapes. Their only option now is to go to a place called Club Hel and confront the Merovingian for Neo's freedom.

Seraph, Morpheus and Trinity enter Club Hel to persuade the Merovingian to release Neo. The Merovingian demands "the eyes of the Oracle" in exchange for Neo's release. Trinity provokes a Mexican standoff, forcing the Merovingian to release Neo. In Mobil Ave, Neo tries to leave by running through the train tunnel. When he does, he simply runs back into the station from the opposite direction. Some time later, Trinity arrives and frees Neo.

Troubled by visions of the Machine City, Neo visits the Oracle. She informs him that as the One, upon visiting the Source (the Machine mainframe), he developed a connection with it. The Matrix and the rest of the Machine world, are derived from the Source as well. Thus we learn that all of Neo's abilities - both in and out of the Matrix - exist because of this connection. This is how Neo was able to stop the machines giving pursuit after the Nebuchadnezzar was destroyed, although the end result of his lack of preparation was temporary confinement in Mobil Avenue.

She characterizes Smith (Hugo Weaving) as Neo's exact opposite and negative, who threatens to destroy the Matrix and the Machine City. She states that "everything that has a beginning has an end", and that the war is about to end. After Neo leaves, a large group of Smiths assimilate Sati, Seraph and the compliant Oracle, gaining her powers of precognition. This also has the effect of destabilizing the Matrix.

In the real world, the remaining crew of the Nebuchadnezzar and the Mjolnir ("Hammer") find Niobe's (Jada Pinkett Smith) ship, the Logos and reactivate it. They also interrogate the now-awakened Bane, who claims he has no memory of the events of the earlier battle. As the captains' plan to return to defend Zion, Neo announces that he needs a ship to travel to the Machine City. The captain of the Hammer refuses, but motivated by her meeting with the Oracle, Niobe offers Neo the Logos. Niobe was told by the Oracle in Enter The Matrix that she would have to make a choice to help Neo or not. Trinity decides to accompany Neo

Niobe pilots the Hammer through service tunnels in order to avoid the Sentinel army. They discover that Bane has murdered a crew member and presumably hidden aboard the Logos but are unable to warn Trinity and Neo since Bane would have control of an EMP and disable both of their ships. Bane ambushes Trinity, taking her hostage. Neo fights Bane and to his horror, realizes he is Smith. Smith blinds Neo by cauterizing his eyes with a power cable. Despite his blindness, Neo sees the glowing form of Smith and kills him. Trinity pilots them to the Machine City.

Niobe, with Morpheus as her co-pilot, flies the Hammer through the lowest tunnel system. Flying slowly and at low power to avoid detection, they make their way to Zion. One of the craft's hover pads collides with the debris on the floor of the tunnel - the bang is heard by the sentinels, who immediately pursue the craft. The crew makes a valiant effort to fight them off, however, they overwhelm the ship and begin to damage it with cutting lasers. A small group of sentinels also rips off the craft's communication's antenna, making it impossible for them to signal Zion they're coming.

In Zion, the defenders deploy Armored Personnel Units tasked with fighting the Sentinels and infantry armed with rocket launchers to destroy the two drilling machines. Zee (Nona Gaye) and her partner manage to take down one of the drills, but the APUs are unable to hold the docks and Captain Mifune (Nathaniel Lees) is fatally wounded. Mifune tells the Kid (Clayton Watson), who has been rearming Mifune's APU, to open the gate for the Hammer. Kid pilots the APU and opens the gate. The Sentinels are on the verge of overwhelming the humans when the Hammer arrives at Zion and discharges its EMP, disabling the Sentinels but also the remaining defenses. The humans are forced to retreat to the temple's entrance and wait for the next attack, which they believe will be their last stand.

Neo and Trinity are attacked by the Machine City's defenses. Neo uses his powers to destroy the incoming weapons, but Sentinels overwhelm the ship. Neo tells Trinity to fly the Logos into an electrical storm cloud, disabling the Sentinels but also the ship's engines. Trinity sees sunlight and blue sky for the first time before the ship free-falls into the Machine City. Trinity fails to restart the ship in time, and it collides with a tower, the impact causing several pieces of the tower to pierce the ship, killing Trinity. Fatally wounded by debris, Trinity declares her love for Neo before dying.

Neo enters the Machine City to bargain with the Machines and their leader, the Deus Ex Machina (Kevin Michael Richardson). Neo warns that Smith is beyond the Machines' control and will assault the Source. He offers to stop Smith in exchange for peace with Zion. The second wave of Sentinels in Zion instantly responds by standing down at the temple entrance.

The Machines agree and order the Sentinels to standby. The Machines provide a connection for Neo to enter the Matrix. In the Matrix, now wholly populated by Smith's copies and in a constant thunderstorm, the clone with the Oracle's powers steps forth, claiming that he has foreseen his victory.

The Smith clones watch while Neo and Smith fight, and as Smith now possesses the power of flight, their battle eventually takes them into the sky, where Smith forcibly drives Neo into a crater. Neo is outmatched but refuses to give up. Seeing Neo's determination, a frustrated Smith continues attacking, but when he repeats the Oracle's words, "Everything that has a beginning has an end", Neo realizes the meaning behind the words and baits Smith into assimilating him.

Since The Matrix was built on balance, with Neo gone, The Smiths cause an imbalance to the system which in turn must destroy them. An energy surge is sent through the connection. The Neo-Smith and the clones burst into light that ripples through the Matrix. After the energy burst, the Oracle's body is shown lying in the crater. In the real world, the Sentinels withdraw from Zion. Neo has sacrificed his life to save the Machines and the humans. The Deus Ex Machina says, "It is done", and Neo's body is carried away by the Machines.

The Matrix "reboots", repairing the damage caused by Neo and Smith's battle. The Architect and the Oracle meet, agreeing that the peace will last "as long as it can" and all the humans who wish to be free from the Matrix will be allowed to leave. Sati, who has created a colorful dawn sky to honor Neo, asks the Oracle whether they will ever see him again. She replies that she thinks they will. Seraph asks the Oracle if she knew this would happen, and she replies that she did not know, but she believed.