In 2028, two years after the intelligent apes revolted against the humans, they are forced to battle a rogue U.S. military faction called Alpha-Omega, led by The Colonel (Woody Harrelson), who employ turncoat apes called Donkeys. A platoon of this group attacks an ape outpost, but four soldiers, including Preacher (Gabriel Chavarria) and a Donkey gorilla named Red (Ty Olsson) are captured. Caesar (Andy Serkis) releases the humans to show that he is not a savage, and Red escapes after attacking an albino gorilla named Winter (Aleks Raunovic).
Caesar’s son Blue Eyes (Max Lloyd-Jones) and lieutenant Rocket (Terry Notary) return from a journey to report that they have found a perfect sanctuary for the apes, across the desert. Winter thinks they must leave immediately, but Caesar wants to prepare first. That night, the Colonel attacks, killing Blue Eyes and Caesar’s wife Cornelia (Judy Greer). They cannot find Winter, who they believe has betrayed them.
The tribe gathers to leave. Caesar leaves his youngest son Cornelius (Devyn Dalton) in the care of Blue Eyes’s widow Lake (Sara Canning), then sets out to act as a decoy. Rocket, the orangutan Maurice (Karin Konoval), and the gorilla Luca (Michael Adamthwaite) accompany him. They enter a desolate place where Caesar kills a soldier in self-defense. They find a mute girl (Amiah Miller), whom Maurice befriends. They also find Winter, now a Donkey at an Alpha-Omega camp. He says the Colonel has left and tries to call for help. He is restrained and Caesar accidentally suffocates him. They find wounded soldiers who are also mute and the Donkey gorilla named Red.
An intelligent ape named Bad Ape (Steve Zahn) shows up, indicating that there are others like them on the planet. He leads them to Alpha-Omega at a fortified quarantine camp in the mountains. Luca is killed and Caesar is captured. His whole tribe is being forced to build a wall, but Caesar inspires them to stop work. It seems the Colonel is putting up barricades to protect him from the rest of the army, after he killed a lot of humans infected with the Simian Flu virus that rendered them mute. He tortures Caesar, but the mute girl sneaks in to give him food and water, along with her rag doll, which the Colonel confiscates. Rocket allows himself to be beaten to protect the girl.
Caesar and Rocket free the apes. Caesar stays behind to confront the Colonel, who now has the Simian Flu himself, caught from the rag doll, and commits suicide. The apes are caught in a crossfire between the two human armies. Caesar is shot by Preacher as he is trying to blow up a fuel tank. Red kills Preacher and is killed himself. Caesar manages to set off the explosion, burying both human armies in a mountain avalanche. The apes cross the Colorado Plateau desert to the oasis. Caesar dies of his wounds and Maurice vows to tell his story to generations of apes unborn.
The film was directed by Matt Reeves from a screenplay by himself and Mark Bomback, produced by Peter Chemin, Dylan Clark, Rick Jaffa, and Amanda Silver. It was released to critical acclaim and was a commercial success. It received nominations from the Oscars and the British Film Academy. Reeves and Bomback watched movies for days for inspiration, including all the original Apes films, war-movies, westerns, The Empire Strikes Back, The Bridge on the River Kwai, The Great Escape, Ben Hur, The Ten Commandments, and Apocalypse Now. A fourth Ape film is being planned. Primatologists were impressed by the apes’ behavior in the movie.
When Maurice speaks to Nova for the first time, it is with the voice of Charlton Heston. The film features many biblical allusions, especially to Exodus. The humans enslave the apes to build walls, but the apes escape to cross a desert to the promised land, but Caesar does not survive to reach it. Caesar is crucified on a cross and dies from a wound in his side. There are also references to the earlier Ape films. An orangutan becomes the Lawgiver. Nova is a mute girl and the whole human species appears to be devolving into a mute species. The apes are crucified on giant X’s like those in the Forbidden Zone. Caesar’s second son is called Cornelius. There is mention of a lost space expedition and at the end, the camera turns to the sky. The end music is atonal, like that of Planet of the Apes.