Caesar's ape tribe has been embroiled in war with a human military faction known as Alpha-Omega. Unwilling to suffer any more casualties, the apes make plans to relocate their clan across the desert. However, on the night before their journey, AO militants infiltrate the apes' base, and their colonel, McCullough, kills Caesar's wife Cornelia and elder son, Blue Eyes. Desiring vengeance, Caesar departs from the tribe to track down McCullough, joined by his close friends, Maurice, Rocket and Luca, leaving the rest of the tribe to continue their journey without them.
During their journey, Caesar's group encounter a man living in an abandoned village and kill him when he reaches for his rifle. They discover the man's daughter, who is unable to speak, and take her in, dubbing her "Nova". Continuing their journey, they arrive at an AO encampment, where they find the traitorous albino gorilla Winter, who confesses to having given up the location of Caesar's base to the colonel out of fear. He also reveals that McCullough is heading to a location called the "border". Caesar inadvertently kills Winter while trying to keep him quiet, causing him to fear he is becoming like Koba, his deceased enemy. Shortly afterwards, Caesar's group find several AO militants who have been executed and abandoned, and learn that they, like Nova, are unable to speak.
Caesar's group comes across a chimpanzee called Bad Ape, who directs them to the border, a former weapons depot turned quarantine facility. Shortly afterwards, Caesar's group is ambushed by an AO patrol, and Luca is killed. Caesar leaves the rest of the group and investigates the border, discovering that the ape tribe has been captured and imprisoned by the AO militants in his absence. Caesar is then captured by Red, a gorilla who has joined forces with the Alpha-Omega. Caesar is brought before McCullough, who explains that the Simian Flu virus has mutated and is rendering those infected mute and regressing to a primitive state. He reveals that he is forcing the apes to build a wall to barricade the border to fend off rival military forces coming to wage war against the Alpha-Omega.
Caesar and the other apes are subjected to starvation from the AO militants. Nova enters the facility and gives Caesar food and water. To prevent her from being discovered, Rocket allows himself to be captured as a diversion. Caesar's group manages to free the other apes and use an underground tunnel as a means to escape the AO facility. During their escape, the rival military faction launches their attack on the facility. In the midst of the chaos, Caesar sets off to confront McCullough, but finds that he has been infected by the mutated virus and spares him. Unwilling to suffer the effects of the virus, McCullough commits suicide.
During the battle between Alpha-Omega and the rival militants, the escaping apes come under fire from AO militants. Caesar attempts to blow up the facility's fuel supplies, but is shot with a crossbow by Preacher, one of the AO militants. Before Preacher can finish Caesar off, he is killed by Red, who is shortly afterwards executed for his betrayal. Caesar then uses a grenade to blow up the fuel supplies, destroying the wall and allowing the rival militants to secure victory. However, an avalanche occurs that buries the rival militants, while the apes and Nova narrowly survive.
With the humans gone, the apes cross the desert and find an oasis, where they settle down. As the apes celebrate, Caesar reveals to Maurice that he is dying of his injuries. Maurice assures Caesar that he will be remembered for his actions as Caesar quietly passes away, content that his tribe is safe.
- Andy Serkis as Caesar.
- Steve Zahn as Bad Ape.
- Karin Konoval as Maurice.
- Terry Notary as Rocket.
- Ty Olsson as Red.
- Michael Adamthwaite as Luca.
- Toby Kebbel as Koba.
- Judy Greer as Cornelia.
- Sara Canning as Lake.
- Devyn Dalton as Cornelius.
- Aleks Paunovic as Winter.