A programmer is brought back to reason and reality when learning he was living in a program created by gigantic machines which make human birth artificial. In order to set humanity free, Neo will have to face many enemies by using technologies and self-trust.

In this second adventure, Neo and the rebel leaders estimate that they have 72 hours until Zion falls under siege to the Machine Army. Only a matter of hours separates the last human enclave on Earth from 250,000 Sentinels programmed to destroy mankind. But the citizens of Zion, emboldened by Morpheus conviction that the One will fulfill the Oracles Prophecy and end the war with the Machines, rest all manner of hope and expectation on Neo, who finds himself stalled by disturbing visions as he searches for a course of action.

Neo discovers that somehow he is able to use his powers in the real world too and that his mind can be freed from his body, as a result of which he finds himself trapped on a train station between the Matrix and the Real World. Meanwhile, Zion is preparing for the oncoming war with the machines with very little chances of survival. Neo's associates set out to free him from The Merovingian since it's believed that he is the One who will end the war between humans and the machines. What they do not know is that there is a threat from a third party, someone who has plans to destroy both the worlds.