Two years after the U.S. military was called to fight off an increasingly intelligent and dangerous tribe of apes, starting a devastating war between the two species, the apes’ clan, led by the chimpanzee Caesar, are attacked in the woods by a rogue paramilitary faction known as Alpha-Omega, led by a mysterious Colonel. Alpha-Omega has in its service apes (called “donkeys”) that had previously followed Koba, a maniacal, human-hating bonobo who led a failed coup against Caesar and started the war after leading a vengeful attack against human survivors in San Francisco.
During Alpha-Omega’s attack, the human soldiers are met by heavy ape resistance. Four soldiers and a “donkey” gorilla named Red are captured by the apes. Caesar arrives and releases the human soldiers, telling them to deliver a message to the Colonel – that he killed Koba for starting the war and that he desires peace between the humans and apes. Caesar then orders that Red be imprisoned but Red escapes, injuring albino gorilla Winter.
Soon after, Caesar’s son, Blue Eyes, and his lieutenant Rocket return from a journey to find a safe haven for the apes. They report that they have found a place across the desert that is perfect for the clan. Winter, still frightened from the soldiers’ attack, wants to leave immediately, but Caesar does not think they are prepared to leave so soon. That night, a group of Alpha-Omega soldiers, led by the Colonel, infiltrates the apes’ home behind a waterfall. The apes discover their presence and kill them all except the Colonel, whom Caesar encounters preparing to escape. Discovering that the Colonel has killed his wife Cornelia along with Blue Eyes, an enraged Caesar lunges at the Colonel but fails to prevent him from escaping out of the waterfall. Upon discovering that Winter has disappeared, Luca, a gorilla and Caesar’s secondary lieutenant, believes that he has betrayed them out of cowardice.
Leaving his younger son Cornelius in the care of Blue Eyes’ mate Lake, Caesar departs to exact revenge on the Colonel for the deaths of his wife and oldest son. He is accompanied by Maurice, a orangutan and Caesar’s adviser, Luca, and Rocket. The other apes head for the desert. During their journey, the apes enter an abandoned village, encounter a soldier, and kill him. Caesar, Maurice, Luca, and Rocket search the dead soldier’s home. Maurice discovers the soldier’s daughter who is apparently unable to speak. Maurice befriends and adopts the girl, giving her a small rag doll.
Caesar’s party eventually sneak inside an Alpha-Omega camp on a beach and encounter Winter, who has volunteered to become a “donkey” for the soldiers in return for sparing his life. He tells Caesar’s group that the Colonel has departed for a location called the “border”, where soldiers further north will meet them. Winter tries to call out to the Alpha-Omega soldiers to save him, and Caesar and the others restrain him from making noise. In the struggle, Caesar accidentally smothers and kills Winter. Caesar begins to worry that he is becoming like Koba by killing his fellow apes and seeking revenge.