Niobe, the captain of the Logos, and Ghost, her first mate, are the first characters we meet. They are tasked with retrieving a package abandoned in the Matrix by the crew of the recently demolished rebel ship Osiris. Ghost and Niobe eventually make their way out of the Matrix with the item, followed by agents. The package contains a warning message sent to the human city of Zion, informing its inhabitants that an army of Sentinels is currently digging its way to Zion. Niobe and Ghost have been tasked with coordinating a defense strategy by bringing the remaining ships back to Zion. During this mission, Niobe and Ghost offer their assistance to a separate set of agents who are attempting to flee the area. Now that everyone is back on board, the captains of the several ships gather in the Matrix to discuss their options for the most effective means of self-defense. Agents launch an assault on the building they are currently meeting in while it is under siege. When everyone else in the Matrix is safe except for Niobe and Ghost, the Keymaker, a computer capable of accessing any region in the Matrix, escorts them to safety through a door he established. Niobe and Ghost helped the humans escape the Matrix. The Keymaker provides the two with a key that they are tasked with delivering to Neo, the main character of the three-part film trilogy.
On the other hand, supporters working for the Merovingian, a program developed in the early stages of the Matrix and now a powerful crime boss in the Matrix, steal the key. Throughout Niobe and Ghost’s pursuit of them, the character that the player did not select would be taken captive by other goons. In order to prevent the player character from rescuing the person who was captured, the Merovingian destroys the key that the Keymaker had given them. They eventually make their way out of the Matrix.
