This story takes place after the events of "The Matrix Revolutions" (2003) but in an alternate timeline where Neo did not die. Morpheus must trek to the Machine City to recover the One, partly corrupted by Smith, while still liberating humans from the freshly rebooted, highly unstable Matrix.

This story takes place in the events between the first and second films in "The Matrix" trilogy after the epiphany of Neo as the One.