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, which turns out to be a message to the human city Zion, warning them that the machines are approaching with an army of Sentinels. Niobe and Ghost are tasked with calling the rest of the ships back to Zion to coordinate a defense.

The Matrix: Path of Neo will follow the story of the blockbuster motion picture trilogy The Matrix, The Matrix Reloaded and The Matrix Revolutions and for the first time allow gamers to play as "Neo" and become "The One."