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
Lock, 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 Lock's orders. The Caduceus receives a message from the
Oracle, and the Nebuchadnezzar, also in defiance of Lock'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 defends himself with
his martial arts proficiencies, but is eventually overwhelmed, covered
by a massive pile of Smith clones. However, he manages to throw them
off and fly 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, at the cost of a passionate kiss from Neo.
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 tells Trinity to escape with the
Keymaker on a motorcycle. Pursued by Agents in a dangerous highway
chase, Trinity gives the Keymaker back to Morpheus, who then saves the
Keymaker from an Agent with help from Niobe. Both Morpheus and the
Keymaker 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
Nebuchadnezzar, 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 Nebuchadnezzar 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, which will reset the
Matrix back to its prime program. Afterwards, he will be asked to
choose 16 females and 7 males to rebuild Zion after the inevitable
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 cause the unresolved Matrix error to spiral out of control, and
result in the death of every human attached to the Matrix. Along with
the final battle at Zion, this would mean 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 Nebuchadnezzar, 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 a pre-emptive 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, with only a handful of survivors
escaping, the Sentinels having destroyed any ship that could not get
away. Only one survivor was found aboard the Caduceus: Bane/Smith. The
film concludes with Neo lying in a medical room - with the
Smith-possessed Bane lying opposite him.
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