The
film's events are immediately following those of The Matrix Reloaded
and assume familiarity with the story of the last two films.
Bane/Smith and Neo are both in an unconscious state. The former is said
to be merely asleep, but neural patterns indicate that Neo is somehow
connected to the Matrix. Morpheus, dispirited after the destruction of
the Nebuchadnezzar and discovering the true nature of the Prophecy at
the end of the last film, starts a search for Neo within the Matrix.
Neo is in fact trapped in a subway station named "Mobil Avenue", a
transition zone between the Matrix and the Source (the Machine
mainframe). At this station, Neo meets a 'family' of programs,
including a girl named Sati. Her 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, and knocks him away from the train.
Seraph contacts Morpheus on behalf of the Oracle, who informs Morpheus
and Trinity of Neo being trapped 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,
where everyone is pointing a gun at someone's head, thus forcing the
Merovingian to release Neo.
Troubled by new visions of the Machine City, Neo decides to visit the
Oracle one last time. She informs him that as the One, he developed a
connection with the Source, the machine mainframe which both the Matrix
and the Machine world are derived from. 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 Sentinels near the end of The Matrix
Reloaded, although his lack of preparation resulted in a temporary
confinement in Mobil Avenue (notably, "Mobil" is an anagram for
"limbo"). She characterizes Smith (who is also growing in power) as his
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 takes leave of the Oracle, a
large group of Smith clones arrive and successfully assimilate the
unresisting Oracle, gaining her powers of precognition.
In the real world, the remaining crew of the Nebuchadnezzar and the
Mjolnir (also referred to as "the Hammer") 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 cannot explain why. Niobe, who was told by
the Oracle that she would have to make a choice to help Neo or not,
lets him take the Logos. Trinity decides to accompany 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. However, they 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 manages to blind Neo by cauterizing
his eyes with a severed electric cable. In spite of his blindness,
however, Neo can see Smith inside Bane as a fiery form, and kills Bane.
Neo releases Trinity, who pilots them towards the Machine City.
In Zion, the defenders deploy infantry armed with rocket launchers and
Armored Personnel Units in order to protect the dock from the incoming
assault. The dock is invaded by a massive horde of Sentinels as well as
two giant drilling machines. The APUs fail to keep the Dock, with their
leader Captain Mifune fatally wounded. With his last breath, Mifune
tells Kid, who was refilling his ammunition supply at the time, to open
the gate for the Mjolnir. Encouraged by Mifune, Kid gains the courage
to fight and open the gate. Just as the remaining humans are about to
be overwhelmed, the Mjolnir, with more Sentinels at tow, 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 fall back to the
temple entrance and wait for the next swarm.
Nearing the Machine City, Neo and Trinity are attacked. Neo uses his
power to destroy the incoming bombs, but Sentinels overwhelm the ship.
To evade them, Trinity flies the Logos up into an electrical storm
cloud. This manages to disable the Sentinels, but also disables the
ship's engines. Above the cloud layer, Trinity gets a glimpse of real
sunlight and blue sky. 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 arms.
Neo emerges into the Machine City to strike a bargain with the
machines, personified by the Deus Ex Machina. Neo warns the machines
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 on
Zion. The machines provide a connection for Neo to enter the Matrix and
confront Smith. The world is now wholly populated by Smith copies - the
clone with the Oracle's powers steps forth, claiming he has already
foreseen his own victory.
The city's population of Smiths stands by and watches while Neo and
Smith square off. Fighting on the streets, through buildings and into
the sky, they finally brawl in a flooded crater. Neo is eventually
outmatched by Smith but refuses to give up the fight, and a frustrated
Smith continues his attack until Neo is too badly hurt to go on. Smith
announces "Everything that has a beginning has an end, Neo." Hearing
the Oracle's parting advice again, Neo baits the scared Smith into
assimilating him. Neo's final words to Smith are, "It was inevitable,"
quoting Smith's oft-spoken admonition.
Smith's assimilation of Neo is seemingly successful, and when the
Oracle-Smith asks Neo-Smith whether it is over, he receives a nod and
smile as reply. Back in the Machine city, Neo's body spasms as a surge
of energy enters his body through the Matrix connection. Starting with
the Neo copy of Smith, a white light begins to rip the clones apart
from the inside out, similar to the destruction of Agent Smith at the
end of The Matrix.
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.
The Architect, upon meeting the Oracle, tells her that she "played a
very dangerous game" by attempting to change the way the Matrix
functioned. The Oracle responds by saying that she understood the risk
and knew it was worth taking. The two reach an agreement to unplug any
humans who want to be freed. The closing shot of the film depicts a new
dawn on the world of the Matrix, free of green tint, created by Sati.
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