Five years after the intense Battle of San Francisco, a battalion of the U.S. Army known as Alpha-Omega is on a relentless quest to locate Caesar's ape colony, aided by apes referred to as "donkeys." During their pursuit, a platoon attempts to assault an ape outpost, but the skilled apes don't back down, resulting in the death of all but four humans and a donkey gorilla named Red. In a surprising act of goodwill, Caesar chooses to release the remaining humans, but Red manages to escape after launching an attack on Winter.
As fate would have it, Caesar's young son, Blue Eyes, along with Rocket, returns from a scouting mission with promising news of an oasis that could provide a safer residence for the apes. However, that night, the nefarious Colonel of Alpha-Omega leads an infiltration of the colony, tragically killing Caesar's wife, Cornelia, and Blue Eyes, mistaking him for Caesar. Meanwhile, Cornelius, Caesar's younger son, narrowly escapes the attack by hiding as the Colonel slips away.
Determined, Caesar, alongside Rocket, Maurice, and Luca, decides to act as decoys to allow their tribe to journey safely to the oasis. In the relics of a deserted village, Caesar is forced to take a human's life in self-defense and discovers his mute daughter, whom Maurice receives permission from Caesar to care for, providing her with a cherished rag doll. An encounter with Winter, who has betrayed the apes by revealing their location to Alpha-Omega, leads to a confrontation, where he discloses that the Colonel plans to meet further military forces to the north.
In a moment driven by grief and vengeance, Caesar inadvertently kills Winter to prevent him from warning the soldiers. As they pursue the Colonel, Caesar's group stumbles upon a scene of devastation, discovering several dead soldiers executed by their own ranks. A surviving soldier, who is unfortunately mute like the girl, reveals more about the Colonel's brutal tactics. The quest takes a surprising turn when they encounter another intelligent ape named Bad Ape, who has grown up in isolation and guides them to a former weapons depot converted into a military base in the mountains.
Tragedy strikes when a human patrol slaughters Luca, inciting a furious response from Caesar, who orders Maurice, Rocket, Bad Ape, and the mute girl to retreat. In an attempt to rescue his captured tribe, Caesar is eventually caught by Red while discovering that the militia is forcing the apes into grueling labor as a way to bolster their defenses against the incoming military forces.
The Colonel chillingly reveals that the Simian Flu has mutated, causing infected humans to regress to primitive states, losing their intelligence. After dealing with the heartbreaking act of killing his infected son, he orders his troops to eliminate all carriers of the disease, leading to escalating violence with his superiors who still believe a cure is possible. The Colonel's brutal reign involves torturing Caesar, leaving him exposed to harsh conditions, but hope emerges when the mute girl, later named Nova by Maurice, bravely sneaks into the facility to provide him with food.
In a calculated move, Rocket allows himself to be captured to keep Nova hidden, teaming up with Caesar to orchestrate a daring escape. As the Colonel confiscates the doll that Nova gifted Caesar, the remaining apes manage to escape through an underground tunnel just as military forces arrive and chaos erupts.
When the battle commences, Caesar tries to fulfill his vengeful desire to eliminate the Colonel, only to find him afflicted by the virus himself after touching Nova's doll. In a moment of mercy, Caesar refrains from killing the Colonel, allowing him to face the consequences of his own actions. Caesar’s final mission ends in tragedy when he tries to blow up a fuel tank and sustains critical injuries at the hands of Preacher, one of the soldiers he had previously freed.
In a transformative turn of heart, Red kills Preacher to save the apes but meets his own demise in the process. Caesar’s act of destruction results in a devastating avalanche that consumes both armies. With their enemy buried in the snow, Caesar manages to escape.
Finally, as the apes and the newly named Nova continue their journey to the oasis, a somber moment arrives when Maurice discovers Caesar’s grave wounds. He assures Caesar that Cornelius will know of the greatness of his father and the sacrifices made for their kind. With his tribe finding sanctuary in their new home, Caesar peacefully passes away, leaving behind a legacy etched in the hearts of those he fought so fiercely to protect.
