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. 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. A hacking system allows players to enter codes, which can unlock special skills, weapons and secrets, such as a 2-player versus mode. In levels involving vehicles, such as driving a car or piloting the Logos, the style of game play depends on the selected player, with Niobe maneuvering the vehicles to avoid obstacles, whilst Ghost takes control of a gun to fight off incoming enemies (although Ghost is required to drive on one level as Niobe is fighting an Agent on a plane as part of a different level). Some levels involve one on one martial arts fighting against single opponents. At any time, players can activate bullet time (called "Focus" in the game) which slows down time, giving players the ability to perform actions such as shooting in midair and dodging bullets. Most levels involve controlling players in a third-person perspective, using guns and fighting skills to defeat opponents and complete level objectives. Players play as either Niobe or Ghost, each of whom have slight variations during their story. The game takes place at roughly the same time as the events in Reloaded. Ghost is the ship's first mate, weapons guru, and a deep-thinking, philosophical assassin. Niobe is the Captain of the Logos, the fastest ship in the rebel fleet.
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Enter the Matrix gives players control of two of the supporting characters from Reloaded and Revolutions, Ghost ( Anthony Wong) and Niobe ( Jada Pinkett-Smith), members of the same group of rebels as Morpheus, Trinity, and Neo, the protagonists of the series.