Ten years after much of mankind was wiped out by the Simian Flu of ALZ-113, Caesar’s ape colony in Muir Woods is a thriving society that has created its own laws, most importantly Ape Shall Never Kill Ape. Caesar takes his son Blue Eyes on his first deer hunt, where the impulsive youth recklessly runs into a grizzly bear and has to be saved by Koba. Caesar returns home to find his mate Cornelia has given birth to another son.
A group of humans who proved immune to the Simian Flu have gathered in the ruins of San Francisco, and with their electricity set to run out in a few weeks a group is sent into Muir Woods to restart its dam. They run into the apes, and the especially aggressive Carver impulsively shoots Rocket’s son Ash, resulting in a tense standoff until Caesar shouts at them to go. The teenage Alexander drops his bag with its sketchbook in the rush to leave.
Koba, still bitter toward all humans after his years of tortuous experiments, insists they need to wipe the group out, but Caesar instead gives them an ultimatum to stay in the city and never enter his territory again, even returning the bag as a sign of good faith. The humans’ leader Dreyfus knows the dam is their only hope, and Alexander’s father Malcolm offers to lead a small group to make a deal with Caesar to let them use it.
The meeting gets off to a rough start with Koba inciting the other apes against Malcolm, but Caesar ultimately agrees as long as they turn over all their guns. Koba is furious at the decision and reminds Caesar all his scars are also “human work” before leading some apes to spy on the other humans, even luring Blue Eyes into his hatred.
The humans are trapped by a cave-in while working on the dam, and Rocket leads the apes to save them. Unfortunately, the camaraderie doesn’t last as it’s discovered Carver snuck a gun in, and Malcolm’s wife Ellie is barely able to salvage the situation by agreeing to use her medical knowledge to help Cornelia, who has gotten sick since her son’s birth.
Koba discovers that the humans have a huge stockpile of assault weapons, and returns accusing Caesar of loving them more than his own kind. Caesar furiously beats Koba but stops short of killing him due to their law, leading to Koba stealing a gun and shooting Caesar, framing Carver for the deed after he’d already been killed. Koba leads the apes in a full assault on the humans, using horses, assault rifles, and even a tank to breach the walls. When Ash refuses an order to kill a captive human, Koba throws him to his death and insists the apes follow his every order, to Blue Eyes’ dismay. He also imprisons all other apes loyal to Caesar in a bus, including Maurice and Rocket.
Malcolm and Ellie find the barely alive Caesar, who directs them to Will’s old house. Malcolm has to sneak back into the colony for medical supplies, and runs into Blue Eyes and brings him back. Father and son both make amends, and Blue Eyes speaks for the first time, asking to help while Caesar recovers. He frees the imprisoned apes and brings them back to the house, where Caesar takes command again for an attack against Koba.
Caesar’s faction sneaks in through the sewer, where Malcolm runs into Dreyfus rigging a massive amount of C4 to destroy Koba’s headquarters. As they argue over how to proceed, Caesar confronts Koba and baits him into another fistfight without guns. Dreyfus ultimately refuses to listen and blows himself up insisting he’s saving the human race, and in the confusion of the explosion Koba gets his gun again and fires on Caesar’s forces. Caesar makes a daring jump toward him and Koba is left dangling from a high beam just like he found Jacobs. He tries to appeal to ape law, but Caesar coldly says “You are not ape” and drops him to his death.
Malcolm emerges and Caesar stops the apes from attacking him. He reveals Dreyfus was able to contact a military outpost who are on their way, to which Caesar tells him to go and save himself. They both regretfully say they really thought there was a chance the two species could co-exist in peace, and as Malcolm leaves with his family, Caesar looks over his army for the coming war.
