The game was written and directed by the Wachowski brothers, and its plot is intertwined with that of the second movie, The Matrix Reloaded.

The player takes the role of Niobe or Ghost, captain and first mate of the rebel ship Logos, respectively. Niobe is a master combatant and an excellent pilot in both the real world and the Matrix.

Ghost is highly skilled with firearms and marksmanship. Both characters are very athletic, and the player must walk, run, jump, strafe, peek, run on walls, climb ladders and pipes, and fight various enemies.