The year is 2029. John Connor, leader of the resistance continues the war against the machines. At the Los Angeles offensive, John's fears of the unknown future begin to emerge when TECOM spies reveal a new plot by SkyNet that will attack him from both fronts; past and future, and will ultimately change warfare forever.

A group of scientists in San Francisco struggle to stay alive in the aftermath of a plague that is wiping out humanity, while Caesar tries to maintain dominance over his community of intelligent apes.