Enter the Matrix
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.
With this in mind, 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, although Niobe and Ghost are able to help their allies escape. They then encounter the Keymaker, a program capable of accessing any area in the Matrix, who leads them to safety through a door he created. The Keymaker gives the two a key that they are supposed to give to Neo. However, the key is stolen by henchmen of the Merovingian, a program created during the early days of the Matrix who now operates an illegal smuggling ring within the program. Ultimately, the Merovingian destroys the key, but Niobe and Ghost are able to escape, when the Keymaker realizes that it is too early for the key to be given to Neo.
Niobe later volunteers to go find the Nebuchadnezzar, the ship captained by Morpheus, upon which Neo serves, and the only ship yet to return to Zion. Upon finding the ship and its crew, and helping them escape from the Matrix, Niobe and Ghost agree to help in Neo's mission against the machines, agreeing to destroy a power plant. After this mission is completed, the Oracle, a program that often gives the humans advice, requests that the player character come and speak to her. After their conversation, the player is confronted by Agent Smith, a rogue Agent that seeks to destroy both the human and machine worlds. The player character barely escapes from the hundreds of Smith copies and the Matrix. Once out, the Logos is attacked by the machines. They defeat the machines by setting off an EMP, which disables their own ship in the process. The game ends with Niobe and Ghost waiting in the Logos, hoping that they will be rescued. The two wonder what's coming but believe that it will be "a hell of a ride."
=== Characters ===
Aside from Ghost and Niobe, there are numerous secondary characters in Enter The Matrix.
Sparks — the operator on the Logos; he gives players tips and information throughout the game.
Smith — a program that can absorb human bodies and humanoid programs to make copies of himself; he chases the player through an abandoned skyscraper, and later, Chinatown.
Agent Johnson — an agent who appears frequently during the game; Niobe defeats him by kicking him off a cargo plane, while Ghost defeats him by knocking him into a short-circuited computer server.
Agent Jackson — another agent with frequent appearances in the game; Ghost defeats him by blowing up his helicopter. Jackson also tries to kill Niobe and Ghost after the crew of the Caduceus is saved, but the two were unexpectedly saved by the Keymaker.
Agent Thompson — the least-featured Agent in the game, who only appears in cinematics; the only opportunity to fight him occurs at the end of Niobe's missions at the power plant.
The Oracle — a program within the Matrix who often helps the humans.
Seraph — a martial arts master who protects the Oracle; he fights Niobe or Ghost once during the events of the game.
Morpheus — a member of the rebels, Niobe's ex-boyfriend, and captain of the Nebuchadnezzar.
Trinity — another rebel, a good friend of Ghost, to whom she refers as "dear brother"; first mate on the Nebuchadnezzar.
Neo — the most important rebel; Morpheus believes he is "The One".
Cmdr. Locke — leader of the Zion defence forces; Niobe's current boyfriend.
Axel, Soren, Ballard, Bane, Vector, Binary, Ice, Corrupt and Malachi — rebels encountered during the game.
The Keymaker — an old program who guides players through certain portions of the game.
The Trainman — carries multiple wristwatches on his arms; he controls the link between the Matrix and the machine city, and works for the Merovingian.
The Merovingian — an old program that has gone rogue in the Matrix; he has a chateau in the mountains wherein he has the Keymaker imprisoned; his henchmen are from early Matrix programs, and are rumored to be "vampires" and "werewolves".
Persephone — wife of the Merovingian; often betrays him out of spite.
Cain and Abel — two henchmen of the Merovingian.
Vlad — the black-clad, pale-skinned leader of the Merovingian's vampires; he is killed by Niobe, who stabs him through the heart with a wooden stake.
Cujo — the leader of the Merovingian's werewolves; he is killed by being impaled on a wooden stake in the dungeons of the chateau.
The Twins — employees of the Merovingian, they are encountered as the player leaves the chateau; they chase the players down a long tunnel, before they are finally evaded.
Sewing Woman — a character featured in the multiplayer mode of the game.
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