Plot
In 2028, two years after the Battle of San Francisco, an American battalion known as "Alpha-Omega" aided by apes derogatorily called "donkeys", searches for Caesar's ape colony. A platoon assaults an ape outpost, but the apes repel the attack and kill all but four humans and a donkey gorilla named Red. Caesar releases the human captives as a peacekeeping gesture, but Red escapes after attacking Winter, an albino gorilla in Caesar's tribe. Caesar's young son Blue Eyes and Rocket return from a scouting expedition to report they have found an oasis that could serve as a safer home. That night, the Colonel of Alpha-Omega leads a team to raid the colony and kills Cornelia and Blue Eyes, mistaking the latter for Caesar. Cornelius, Caesar's younger son, manages to survive the attack by hiding while the Colonel escapes.
Caesar, followed by Rocket, Maurice, and Luca, decide to serve as decoys while the tribe journeys to the oasis. In an abandoned village, Caesar kills a human in self-defense and finds his mute daughter, whom Maurice - with Caesar's consent - takes guardianship of, giving her a rag doll. They encounter Winter, now working for Alpha-Omega after giving away their hideout, having faked the attack by Red and letting him escape, and confront him. He reveals that the Colonel is heading north to meet up with the rest of the military forces. Caesar prevents him from alerting the soldiers, but accidentally kills Winter in retribution for his wife and son. As they follow the Colonel, Caesar's group discovers several dead soldiers executed by their own troops; a fatally wounded survivor is revealed to be mute, just like the girl.
Caesar's group chases someone who has stolen one of their horses and discovers the thief is another intelligent ape, Bad Ape, who grew in isolation. He guides them to a former weapons depot-turned quarantine facility in the mountains that serves as the base for the militia. Soldiers kill Luca, and an enraged Caesar tells Maurice, Rocket, Bad Ape, and the mute girl to turn back. Caesar attempts to infiltrate the base alone, but he discovers his tribe has been captured and forced into labor there before Red catches him. Caesar deduces that the Colonel and militia are using the apes to barricade the facility to fend off the incoming military forces, which intend to attack rather than reinforce the militia.
The Colonel reveals that the Simian Flu virus has mutated, causing infected humans to devolve into primitive animals, depriving them of their intelligence and ability to speak. After killing his infected son, he ordered his own troops to kill any carriers before they could infect others. This led to a conflict with his superiors, who believed the disease could still be cured, and are coming to forcibly relieve the Colonel of his command. The Colonel has Caesar tortured, starved, and leaves him exposed to the cold. The mute girl, named Nova by Maurice, sneaks into the facility to feed Caesar. Rocket allows himself to be captured to prevent Nova from being seen and so he and Caesar can formulate a plan to escape. The Colonel later confiscates the doll Nova left for Caesar, but the other apes escape via an underground tunnel.
The military arrives and attacks the facility, and the apes are caught in the crossfire. During the chaos, Caesar sneaks into the Colonel's quarters to kill him, only to find that the virus has infected him after handling Nova's doll. Caesar refuses to kill the Colonel, instead allowing him to kill himself. Caesar then attempts to destroy a fuel tank but is wounded by Preacher, a sergeant he released earlier, with a crossbow. At the sight of the apes being killed, Red redeems himself by killing Preacher with a grenade launcher before being executed. Caesar blows the fuel tank, causing an avalanche that buries both armies as he flees up the trees with the rest of the apes and Nova.
The apes and Nova resume their journey to the oasis. As they arrive, Maurice discovers Caesar's wound and promises that Cornelius will know who his father was and what he did for the apes. With his colony safe in their new home, Caesar peacefully passes away.
