The game's story picks up just before The Matrix Reloaded and runs parallel to that of the film. Bend the rules of the Matrix with martial arts, pilot the fastest hovercraft in the fleet, or just fight with lots of guns.
A man is rescued by a lifeguard on Brighton Beach. He has suffered a head wound and has no memory of who he is. His only clues to his identity are a tattoo of a roman numeral, XIII and a key to a bank deposit box.
A proud yet innocent prince is being chased by The Dahaka (Guardian of Time) as a consequence of his actions. He seeks aid from The Empress of Time to escape from the notion that he cannot change his fate.