Seems the “Enter the Matrix” video-game is a bit spoilerish with reference to the next installment of the movie series. There’s an hour or so of footage that the Wachowski’s have filmed specifically for the game and seems it’s a rather giving guide to future events in the film series – beware.
A scooper for Dark Horizons writes:
"The Oracle (played by an actress named Mary Alice, due to Gloria Foster’s death; I assume this means that Mary Alice will play the Oracle in Revolutions, as well) states that a "special child" who will "change the world" is the child of two programs similar to herself. If she means Neo, this would suggest that Neo is a program and thus that Zion is still part of the Matrix. The Oracle says the two programs betrayed her for their love by giving Merovingian (the French information-collector guy, played by Lambert Wilson) her termination key. The Oracle allowed this because she wanted the programs to have their special child.
A hobo with longish blond hair who also appears in the Revolutions trailer has a conversation with Niobe (Jada Pinket-Smith) in which he reveals that the Zion before this one "only lasted 72 hours". Niobe volunteered to be the second ship to enter the Matrix and contact the Nebuchadnezzar because her boyfriend, Command Lock revealed to her that he had arranged for her ship, the Logos, to be the only one not to participate in the defense of Zion, in order to protect her, and she was angry. At the end of the events of Reloaded, Niobi and Ghost’s hovercraft (Logos) has crashed in an uncharted underground area and they do not know how they will be found and rescued".