The story begins with Niobe, captain of the Logos, and Ghost, her first mate, retrieving a package left in the Matrix by the crew of the recently destroyed rebel ship Osiris. After being pursued by Agents, Ghost and Niobe escape from the Matrix with the package.

The package is a message to the human city Zion, warning them that the machines are tunneling to Zion with an army of Sentinels. Niobe and Ghost are tasked with calling the rest of the ships back to Zion to coordinate a defense. During this operation, Niobe and Ghost provide backup to another group of operatives trying to escape.

With everyone home, the captains of the various ships hold a meeting in the Matrix to decide on how best to defend themselves. During the meeting, Agents attack the building they are in. Niobe and Ghost help the humans escape; when everyone is safe except them, the Keymaker, a program capable of accessing any area in the Matrix, leads them to safety through a door that he created.

The Keymaker gives the two a key that they are supposed to give to Neo, the protagonist of the film trilogy. However, the key is stolen by henchmen of the Merovingian, a program created during the early days of the Matrix who now is a crime boss in the Matrix. As Niobe and Ghost pursue them, the character that the player did not choose is captured by more henchmen. Before the player character rescues the one captured, the Merovingian destroys the key that the Keymaker gave them. They then escape from the Matrix.