In this third version of the Planet of the Apes film, it has been 15 years since the ALZ-113 virus - also known by the human survivors as as the Simian Flu - spread across the globe killing billions of people (Rise of the Planet of the Apes), leading to a rise of intelligent apes. Their leader, the chimpanzee Caesar (Andy Serkis), had tried to maintain peace between the apes and humans, until the chip Koba (Toby Kebbell) betrayed the apes and brought on the dawn of a new conflict (Dawn of the Planet of the Apes). Now, Caesar and his clan are hiding out in a command base in the Muir Woods while a ruthless Special Forces Colonel of the military faction Alpha-Omega is out to get them. The humans and apes are now caught up in all-out war.
A team of soldiers quietly move through the woods to locate the apes. They are being helped by an ape named Red (Ty Olsson), whom the soldiers refer to as "Donkey". Red and another ape loyal to Koba look out for the command base. The soldiers launch their attack on the base by opening fire, but the apes retaliate with great force, hurling spears and shooting at soldiers as they ride on horses. Red, along with several surviving soldiers, are captured. Caesar decides to spare them and send them back to their camp unharmed to send the message that the apes are peaceful. Red, meanwhile, escapes from the hold of Winter (Aleks Paunovic) and runs back to the camp.
Caesar's son Blue Eyes (Max Lloyd-Jones) returns home to his family and his mate Lake (Sara Canning). Caesar rejoins his wife Cornelia (Judy Greer) and youngest son Cornelius (Devyn Dalton). Caesar and his friends discuss a plan to move the clan away from the woods and toward a new home.
That night as the apes are asleep, several Alpha-Omega soldiers, led by Colonel McCullough (Woody Harrelson), stalk the command base. The soldiers are killed, but McCullough shoots and kills Cornelia and Blue Eyes, having intended to kill Caesar. Caesar finds his family dead and leaps after McCullough as he gets away through the waterfall. McCullough then severs the rope and lets Caesar fall.
Caesar returns to his base and has the other apes search for Cornelius. Thankfully, Caesar finds him safe. He places his son in Lake's care as he heads off to find McCullough while the rest of the apes head toward the desert in search of their new home. Caesar is followed by orangutan Maurice (Karin Konoval), chimp Rocket (Terry Notary), and gorilla Luca (Michael Adamthwaite). Caesar refuses to allow them to join him, but they insist as they want to protect their leader.
The four apes come across a military camp. They find Winter, who has defected to the humans' side after Red promised he would be spared if Winter let him go, which lead Red to tell McCullough where to find the apes. Caesar interrogates Winter and learns that McCullough and his army are talking about heading toward a border. The apes then see that the humans are close. Caesar puts his hand over Winter's mouth to keep him quiet, and he ends up leaving him unconscious.
At night, Caesar has a nightmare about Koba, who appears bloody and more scarred than before. He repeats to Caesar his final words - "Ape not kill ape."
The apes continue heading forward. They encounter a lone man who attempts to shoot them, but Caesar kills him first. They enter his home and find a little girl - later named Nova - (Amiah Miller) lying in bed. Although she appears frightened, Maurice gently hands her a doll. Nova tries to speak but is unable to. The apes proceed to continue their journey, but Nova steps out and sees the dead man (he was possibly her father). Despite Caesar saying they cannot take her, Maurice says he cannot leave her there either.
The apes and Nova pass through the snowy mountains. They find the bodies of three soldiers shot in the snow. One of them is still alive but is slowly dying. Caesar asks him why he was shot, but the soldier cannot speak just like Nova. Maurice points out that the man will die of his wounds, so Caesar puts him out of his misery.
As the apes are looking around the area, a small creature in a jacket steals a rifle and one of the horses. The apes chase after the creature until they corner it in an abandoned building. It is a small ape, known as Bad Ape (Steve Zahn). He offers his jacket to Nova, seeing that she is cold. Bad Ape is capable of speech like Caesar. He tells Caesar that he lived in a zoo before the Simian Flu struck, and he got his name from what the humans always yelled at him. Bad Ape gives the group food that is labeled "California Border". Caesar asks where the food came from, and Bad Ape says it came from a "human zoo" (quarantine camp).
Once the apes reach the military camp, they are attacked by a soldier. Luca kills the solider but is also mortally wounded in the process. Luca tells Caesar that at least he was able to protect him this time. Even Nova cries for Luca as he had shown her kindness before. Caesar tells the others that this is why he wanted to come alone. Maurice tells Caesar that his hatred for the Colonel is making him like Koba.
Caesar heads toward the camp at night by himself, only to find two captured apes hung up on a mountain overlooking the camp. One ape tells Caesar that the ape clan has been captured and are being forced to work. Red then appears behind Caesar and knocks him out with the butt of his rifle.
Caesar wakes up to find himself face-to-face with McCullough. Caesar tells him he came for him after he killed Caesar's family. McCullough gives an insincere apology and says he meant to kill Caesar.
Caesar is put to work with the rest of his captured apes. He sees Lake and Cornelius in a separate cage, with the little ape helplessly calling out for his father. The apes are then forced to work to build a wall, despite being starved and dehydrated. One ape is then whipped by Red, with Caesar yelling at him to stop. Caesar is whipped in his place. McCullough demands that Caesar tell the apes to continue working even as Caesar pleads for him to give them food and water. McCullough kills one ape and prepares to kill more, but Lake and the other apes continue to work for Caesar's sake.
Red and a soldier called Preacher (Gabriel Chavarria) escort Caesar to McCullough's office in chains. Caesar once again tells the Colonel to give the apes food and water. He tells McCullough that he has no mercy. The Colonel verbally hits back that Caesar had shown up with the intention to kill him, but Caesar responds that he did show mercy by sparing his soldiers. McCullough then tells Caesar about his son, who was a soldier in his army until he was affected by the Simian Flu and began to lose his voice, along with other soldiers. McCullough killed his son and those soldiers as he knew they were regressing into a primitive state. He then explains that the wall is meant for another military force that is coming for him to put an end to his radicalized faction.
The captured apes are finally given food and water, except for Caesar. He has another hallucination of Koba, who tells Caesar to join him. Meanwhile in the distance, Maurice, Rocket, Bad Ape, and Nova are seeing what's going on in the camp. Nova walks into the camp and approaches Caesar's cage. She gives him food and water, as well as the doll that Maurice gave her. The soldiers are approaching, and, fearing that they will kill Nova, Rocket steps in as a distraction to allow her to get away. The soldiers capture Rocket and McCullough picks up Nova's doll, which is now stained with blood.
Maurice and Bad Ape find a way to sneak into the camp via an underground tunnel. They proceed to dig through but stop when they hit a water source, fearing it will flood the tunnel. They manage to seal off that part to prevent the flooding.
Caesar and Rocket work together to find a way to make it to the other cage to save the ape children while Maurice and Bad Ape dig their way to the camp. Rocket creates a diversion by flinging poo at one of the guards before Bad Ape pulls him underground. The apes get the children out and make it through the tunnel to get away from the camp. Caesar embraces Cornelius upon seeing him again. Before leaving, Caesar admits to Rocket that he is like Koba because he cannot let go of his hatred for the Colonel. He heads back to McCullough's office to finish his mission.
Soon, the rival military force begins attacking the camp, launching rockets at the soldiers while they fire back. Caesar makes it to McCullough's office and finds him drunk. He tries to speak but he has lost his voice too. Caesar grabs a gun, and the Colonel takes Caesar's hand to hold it to his head, ready for Caesar to pull the trigger. However, Caesar cannot bring himself to do so. McCullough grabs the gun and shoots himself in the head.
In the midst of the chaos, the other apes have gotten away while Caesar tries to rejoin them. He grabs a grenade belt and tries to throw one at a leaking fuel tank, but he is shot with an arrow by Preacher. Red sees this as one of the soldiers is demanding a grenade launcher from him. Red turns on the humans and fires a grenade at Preacher before he finishes Caesar. Red is then shot dead after redeeming himself. Caesar grabs the grenade and finishes the job, destroying the tank and blowing up the whole facility as he gets away through the tunnel.
Caesar reaches the apes as the other militants cheer the fall of Alpha-Omega's camp. Some soldiers spot Caesar and are prepared to shoot him until an avalanche starts coming down. Caesar and the others apes (plus Nova on Maurice's back) climb up the trees to safety while the avalanche wipes out all the remaining soldiers.
The apes and Nova then continue on their journey to a new home until they finally reach a new land that the apes are happy with. Caesar and Maurice watch as the apes are celebrating their freedom, but Maurice notices Caesar's arrow wound. Knowing that he is going to die, Caesar asks Maurice to make sure Cornelius is protected. Maurice assures him that his son will know who he was and what he did for his family. With that, Caesar passes away in peace.