In a world where machines derive their power from unconscious human slaves who exist in a fabricated reality that seems normal to them, a growing number of freed slaves - including Councillor Hamman (ANTHONY ZERBE) and Commander Lock (HARRY LENNIX) -- hope to overthrow their former machine-based oppressors.
Things aren't looking good, however, as the machine world has sent a quarter of a million robotic sentinels to find the escapees and destroy them and their world that's known as Zion. Accordingly, Lock isn't happy that the crew of the Nebuchadnezzar - consisting of leader Morpheus (LAURENCE FISHBURNE), now all-powerful student Neo (KEANU REEVES), ally Trinity (CARRIE-ANNE MOSS) and pilot Link (HAROLD PERRINEAU) -- has been following their own course of action, including visiting the Matrix.
As they and the rest of the humans prepare for battle, Neo must also contend with Agent Smith (HUGO WEAVING), the anthropomorphic physical representation of the machine world who has similarly managed to escape the Matrix and wants his revenge on "The One."
After an encounter with him and his many duplicates, Neo visits the Oracle (GLORIA FOSTER), who informs him that they'll need to find the Key Maker (RANDALL DUK KIM) if they want to succeed. Unfortunately, he's been kidnapped by the powerful Merovingian (LAMBERT WILSON) and his goons.
From that point on, and with the help of Lock's lover, Niobe (JADA PINKETT SMITH), and Merovingian's wife, Persephone (MONICA BELLUCCI), Neo and his allies set out to do what they can to stop the machines and save humanity.