Many generations after Caesar’s death, apes have formed various clans while humans have regressed to a primitive, mute state. Noa, a young chimpanzee from a falconry clan, prepares for his coming-of-age by collecting wild eagle eggs with friends Anaya and Soona. A human scavenger follows them and accidentally breaks Noa’s egg. While searching for a replacement, Noa encounters ape raiders wielding electric weapons who follow his horse back to his village. Noa returns to find his village in flames, his father Koro killed by the gorilla general Sylva. Noa’s clan is abducted, and he sets out to rescue them.

Joined by Raka, an orangutan who shares Caesar’s teachings, they are trailed by the human scavenger, whom Raka names Nova. Nova, revealed to be intelligent and named Mae, tells them the raiders took Noa’s clan to a beachfront settlement near an old human vault. They are ambushed by Sylva on a bridge, and Raka is swept away while saving Mae. Noa and Mae are captured and taken to the apes’ settlement, where Noa meets Proximus Caesar, who enslaves other clans to open the vault for human technology. Proximus believes Noa’s intelligence can help and warns him about Mae’s hidden agenda.

Mae reveals her goal to find a book to restore human speech, and they plan to destroy the vault. Noa, Mae, Soona, and Anaya plant explosives, but Trevathan, a speaking human prisoner, catches them. Mae kills Trevathan, and they enter the vault, finding weapons and a satellite deciphering key, not a book. They discover old books showing humans as the dominant species. Proximus and his tribe confront them; Mae kills Proximus’ lieutenant Lightning and triggers the explosives, flooding the bunker. Mae escapes, and Noa’s clan fights off Proximus, leading to his fall into the sea.

Noa’s clan returns to rebuild, and Mae bids farewell, having destroyed the bunker to prevent the apes from accessing its weapons. They question the possibility of peaceful coexistence between apes and humans. Noa and Soona look through a telescope as Mae reaches a human settlement, delivering the decipher key to reactivate satellites and contact other intelligent humans.