In a dystopian future where machines have enslaved humanity within a simulated reality known as the Matrix, the rebel crew of the hovercraft Nebuchadnezzar is on a mission to ensure the survival of the last human city, Zion. The city is under threat of attack from a massive machine army digging towards it. Neo, the ship's crew member who has unique abilities within the Matrix due to his identity as the prophesied One, seeks a way to end the war between humans and machines. He experiences visions of a disastrous future and seeks answers from the Oracle, hoping to avert the impending calamity.

The rebels face increased opposition from Agents, computer programs that enforce order within the Matrix and prevent the escape of enslaved humans. Agent Smith, now a rogue program with new powers and the ability to replicate himself, becomes a wild card in this struggle. As Neo delves deeper into the complexities of his role, the rebels engage in a series of missions within the Matrix to gain tactical advantages over their enemies and to discover the key to peace. The intricacies of the virtual world and the physical threats outside it converge as the fate of both humanity and the Matrix hang in the balance during these crucial operations.