In a world where machines derive their power from unconscious human slaves who exist in a fabricated reality that seems normal to them, a rebellious set of escaped humans are preparing to make one last stand against the machines and their robotic sentinels.
Various members of the group, including Morpheus (LAURENCE FISHBURNE) and Trinity (CARRIE-ANNE MOSS), want to know how their chosen leader, Neo (KEANU REEVES), managed to enter the fabricated Matrix without being directly plugged into it. At the same time, they're wary of Bane (IAN BLISS), a crewmember who ended up simultaneously unconscious with Neo.
Looking for answers, Morpheus and Trinity meet with the all-knowing Oracle (MARY ALICE) who sends them, along with her bodyguard, Seraph (COLLIN CHOU), to find Neo's imagined self who's trapped in a purgatory of sorts where the Trainman (BRUCE SPENCE) won't let him reenter the Matrix. It turns out the powerful Merovingian (LAMBERT WILSON) has cast Neo there for all eternity.
The others end up freeing him, however, and soon prepare for the pending onslaught of robotic sentinels. As Captain Mifune (NATHANIEL LEES) prepares the ground forces that include Zee (NONA GAYE), The Kid (CLAYTON WATSON) and many others, and Morpheus, his former lover, Niobe (JADA PINKETT SMITH), Trinity and Link (HAROLD PERRINEAU) take to the air, Neo sets out to uncover the secrets behind the Matrix.
While doing so, he must also contend with Agent Smith (HUGO WEAVING), the anthropomorphic physical representation of the machine world who has similarly managed to escape the Matrix, wants his revenge on "The One," and is growing more powerful every day.