Neo, Morpheus, Trinity, and the rest of their crew continue to battle the machines that have enslaved the human race in the Matrix. As their quest unfolds, Neo learns more about his superheroic abilities, including the ability to see the codes of the people and things around him. Now, more humans are waking up out of the Matrix and attempting to live in the real world. As their numbers grow, the battle moves to Zion – the last real-world city and the center of human resistance.

Neo and the rebel leaders estimate that they have 72 hours until 250,000 probes discover Zion and destroy it and its inhabitants. During this, Neo must decide how he can save Trinity from a dark fate in his dreams.