The film's events immediately follow those of The Matrix Reloaded and assume familiarity therewith.
Bane/Smith and Neo are both in an unconscious state. Both men appear to be asleep, but neural patterns show a Matrix similarity in Bane and true Matrix patterns in Neo. Morpheus starts a search for Neo within the Matrix. Neo is trapped in a subway station named "Mobil Avenue," a transition zone between the Matrix and the Source (the Machines' mainframe). At this station, Neo meets a 'family' of programs, including a girl named Sati, whose father tells Neo that Mobil Avenue is controlled by a program called the Trainman who is an exile loyal only to the Merovingian. When Neo tries to board the train with the family, the Trainman refuses to let him aboard.
Seraph contacts Morpheus on behalf of the Oracle. The Oracle, now bound in a new shell as the previous one was d
eleted, informs Morpheus and Trinity of Neo's confinement in Mobil Avenue. Seraph, Morpheus, and Trinity pursue the Trainman to secure Neo's release, but he escapes. The trio enter Club Hel to confront the Merovingian for Neo's freedom. The Merovingian demands "the eyes of the Oracle" in exchange for Neo's release. Trinity loses her patience and provokes a Mexican standoff, forcing the Merovingian to release Neo.
Troubled by new visions of the Machine City, Neo decides to visit the Oracle. She informs him that as the One, he has developed a wireless connection with the Source. All of Neo's abilities - inside and outside the Matrix - exist because of this connection. She also explains Neo's early frustration at the knowledge of the true prophecy, and that he chose not to be ready to accept the truth. She characterizes Smith, who is also growing in power, as Neo's exact "opposite" and his "negative", who threatens to destroy the Machine City as well as the Matrix. She tells Neo cryptically that "everything that has a beginning has an end", and that the war is about to end "one way or another". After Neo leaves the Oracle, a large group of "Smiths," who had already assimilated Sati, arrive and assimilate the unresisting Oracle, gaining her powers of precognition.
In the real world, the remaining crew of the Nebuchadnezzar a
nd the Mjolnir encounter Niobe's deactivated ship, the Logos, and its crew. They successfully reactivate the ship and begin to interrogate the now awakened Bane, who claims he has no memory of the events of the earlier battle. After contemplating his visions, Neo announces that he needs a ship to travel to the Machine City, although he does not explain his reasons. Niobe, acting on the Oracle's prophecy for her, gives him the Logos. Trinity accompanies Neo.
The remaining crews plan to return to Zion and avoid the Sentinel army by allowing Niobe to pilot the Mjolnir through a series of service tunnels, which are nearly impossible to navigate. Shortly after departure, they discover that Bane has murdered a crew member and has hidden aboard the Logos. They also come to realise that Bane was the one who fired the EMP that sabotaged the attack but are unable to warn Trinity and Neo. Before the Logos can depart, Bane ambushes Trinity and takes her hostage. Neo fights Bane, who reveals himself to be a manifestation of Smith. During the struggle, Bane blinds Neo by cauterizing his eyes with a severed power cable. In spite of his blindness, Neo can see Smith inside Bane as a fiery form and kills him. Neo then releases Trinity, who pilots them towards the Machine City. Neo's ability to see artificial intelligence as fiery presences compensates, at least in their vicinity, for his loss of ordinary sight, enabling him to interact with the Machines and their City with as much ability as if he were not blinded.
In Zion, the defenders deploy infantry armed with rocket launchers and Armored Personnel Units (mechanical ba
ttle armor equipped with artillery). The dock is invaded by a massive horde of Sentinels and two giant drilling machines. The APUs fail to defend the Dock, and their leader Captain Mifune is fatally wounded. With his last breath, Mifune tells Kid, who is refilling his ammunition supply, to open the gate for the Mjolnir. Encouraged by Mifune, Kid opens the gate. When the remaining humans are about to be overwhelmed, the Mjolnir, with more Sentinels in pursuit, arrives at Zion and sets off an EMP that disables all the Sentinels as well as the remainder of Zion's defenses. The humans are forced to retreat to the temple's entrance and wait for the next assault.
Nearing the Machine City, Neo and Trinity are attacked by the city's huge defense machines. Neo uses his power to destroy the incoming bombs, but Sentinels overwhelm the ship. To evade them, Trinity flies the Logos into an electrical storm cloud. Her actions disable the Sentinels, but also disable the ship's engines. Above the cloud layer, Trinity sees a glimpse of sunlight and blue sky for the first time. The ship then free-falls directly toward the Machine City, and despite Trinity's attempts to ignite the engines in time, the ship crashes. The impact of the collision fatally wounds Trinity, and she dies in Neo's embrace.
Neo emerges into the Machine City to strike a bargain with the Machines, personified by the Deus Ex Machina, whom he warns that Smith (who has by now assimilated every human and program within the Matrix) is beyond the Machines' control and will soon assault the Source. He offers to help stop Smith in exchange for a ceasefire with Zion. The Machines provide a connection for Neo to enter the Matrix and confront Smith. In the Matrix, which is now wholly populated by Smith's copies, the clone with the Oracle's powers steps forth, claiming that he has already foreseen his own victory.
The city's population of Smiths stands by and watches while Neo and the Oracle/Smith fight on the streets, through buildings, and in
the sky, until they finally brawl in a flooded crater. Neo is eventually outmatched by Smith but refuses to give up the fight. A frustrated Smith continues to attack, but when he reminds Neo "Everything that has a beginning has an end," Neo baits Smith into assimilating him. Smith's assimilation of Neo is seemingly successful, but in the Machine city, Neo's body spasms as a surge of energy enters his body through the Matrix connection. Now connected to the source, Smith can now be deleted by the machines as the copy of Smith that has assimilated Neo, and all the others, are destroyed from the inside out.
With the elimination of the Smiths, all the programs and humans that were possessed return to normal, including the Oracle. The Sentinels that are about to attack withdraw from Zion. Neo, having sacrificed himself to save both the Machines and humans, is unplugged from the Matrix and his body is respectfully carried away by the Machines. A glowing energy coming from Neo implies that he has become "the Source"
The Architect and the Oracle agree to unplug all humans who want to be freed. The closing shot of the film depicts a new dawn created by Sati on the world of the Matrix, which is now free of its characteristic green tint.
Bane/Smith and Neo are both in an unconscious state. Both men appear to be asleep, but neural patterns show a Matrix similarity in Bane and true Matrix patterns in Neo. Morpheus starts a search for Neo within the Matrix. Neo is trapped in a subway station named "Mobil Avenue," a transition zone between the Matrix and the Source (the Machines' mainframe). At this station, Neo meets a 'family' of programs, including a girl named Sati, whose father tells Neo that Mobil Avenue is controlled by a program called the Trainman who is an exile loyal only to the Merovingian. When Neo tries to board the train with the family, the Trainman refuses to let him aboard.
Seraph contacts Morpheus on behalf of the Oracle. The Oracle, now bound in a new shell as the previous one was d
eleted, informs Morpheus and Trinity of Neo's confinement in Mobil Avenue. Seraph, Morpheus, and Trinity pursue the Trainman to secure Neo's release, but he escapes. The trio enter Club Hel to confront the Merovingian for Neo's freedom. The Merovingian demands "the eyes of the Oracle" in exchange for Neo's release. Trinity loses her patience and provokes a Mexican standoff, forcing the Merovingian to release Neo.Troubled by new visions of the Machine City, Neo decides to visit the Oracle. She informs him that as the One, he has developed a wireless connection with the Source. All of Neo's abilities - inside and outside the Matrix - exist because of this connection. She also explains Neo's early frustration at the knowledge of the true prophecy, and that he chose not to be ready to accept the truth. She characterizes Smith, who is also growing in power, as Neo's exact "opposite" and his "negative", who threatens to destroy the Machine City as well as the Matrix. She tells Neo cryptically that "everything that has a beginning has an end", and that the war is about to end "one way or another". After Neo leaves the Oracle, a large group of "Smiths," who had already assimilated Sati, arrive and assimilate the unresisting Oracle, gaining her powers of precognition.
In the real world, the remaining crew of the Nebuchadnezzar a
nd the Mjolnir encounter Niobe's deactivated ship, the Logos, and its crew. They successfully reactivate the ship and begin to interrogate the now awakened Bane, who claims he has no memory of the events of the earlier battle. After contemplating his visions, Neo announces that he needs a ship to travel to the Machine City, although he does not explain his reasons. Niobe, acting on the Oracle's prophecy for her, gives him the Logos. Trinity accompanies Neo.The remaining crews plan to return to Zion and avoid the Sentinel army by allowing Niobe to pilot the Mjolnir through a series of service tunnels, which are nearly impossible to navigate. Shortly after departure, they discover that Bane has murdered a crew member and has hidden aboard the Logos. They also come to realise that Bane was the one who fired the EMP that sabotaged the attack but are unable to warn Trinity and Neo. Before the Logos can depart, Bane ambushes Trinity and takes her hostage. Neo fights Bane, who reveals himself to be a manifestation of Smith. During the struggle, Bane blinds Neo by cauterizing his eyes with a severed power cable. In spite of his blindness, Neo can see Smith inside Bane as a fiery form and kills him. Neo then releases Trinity, who pilots them towards the Machine City. Neo's ability to see artificial intelligence as fiery presences compensates, at least in their vicinity, for his loss of ordinary sight, enabling him to interact with the Machines and their City with as much ability as if he were not blinded.
In Zion, the defenders deploy infantry armed with rocket launchers and Armored Personnel Units (mechanical ba
ttle armor equipped with artillery). The dock is invaded by a massive horde of Sentinels and two giant drilling machines. The APUs fail to defend the Dock, and their leader Captain Mifune is fatally wounded. With his last breath, Mifune tells Kid, who is refilling his ammunition supply, to open the gate for the Mjolnir. Encouraged by Mifune, Kid opens the gate. When the remaining humans are about to be overwhelmed, the Mjolnir, with more Sentinels in pursuit, arrives at Zion and sets off an EMP that disables all the Sentinels as well as the remainder of Zion's defenses. The humans are forced to retreat to the temple's entrance and wait for the next assault.Nearing the Machine City, Neo and Trinity are attacked by the city's huge defense machines. Neo uses his power to destroy the incoming bombs, but Sentinels overwhelm the ship. To evade them, Trinity flies the Logos into an electrical storm cloud. Her actions disable the Sentinels, but also disable the ship's engines. Above the cloud layer, Trinity sees a glimpse of sunlight and blue sky for the first time. The ship then free-falls directly toward the Machine City, and despite Trinity's attempts to ignite the engines in time, the ship crashes. The impact of the collision fatally wounds Trinity, and she dies in Neo's embrace.
Neo emerges into the Machine City to strike a bargain with the Machines, personified by the Deus Ex Machina, whom he warns that Smith (who has by now assimilated every human and program within the Matrix) is beyond the Machines' control and will soon assault the Source. He offers to help stop Smith in exchange for a ceasefire with Zion. The Machines provide a connection for Neo to enter the Matrix and confront Smith. In the Matrix, which is now wholly populated by Smith's copies, the clone with the Oracle's powers steps forth, claiming that he has already foreseen his own victory.
The city's population of Smiths stands by and watches while Neo and the Oracle/Smith fight on the streets, through buildings, and in
the sky, until they finally brawl in a flooded crater. Neo is eventually outmatched by Smith but refuses to give up the fight. A frustrated Smith continues to attack, but when he reminds Neo "Everything that has a beginning has an end," Neo baits Smith into assimilating him. Smith's assimilation of Neo is seemingly successful, but in the Machine city, Neo's body spasms as a surge of energy enters his body through the Matrix connection. Now connected to the source, Smith can now be deleted by the machines as the copy of Smith that has assimilated Neo, and all the others, are destroyed from the inside out.With the elimination of the Smiths, all the programs and humans that were possessed return to normal, including the Oracle. The Sentinels that are about to attack withdraw from Zion. Neo, having sacrificed himself to save both the Machines and humans, is unplugged from the Matrix and his body is respectfully carried away by the Machines. A glowing energy coming from Neo implies that he has become "the Source"
The Architect and the Oracle agree to unplug all humans who want to be freed. The closing shot of the film depicts a new dawn created by Sati on the world of the Matrix, which is now free of its characteristic green tint.