In this sequel to 'Rise of the Planet of the Apes', almost a decade has passed since the outbreak of the ALZ-113 virus which then spread across the globe. The human population has mostly died off from the virus and from violence, while the ape population has thrived and grown. A montage of news reports is shown on a globe crisscrossed with red lines, with footage of escalating violence among humans that has also contributed to the chaos.
Caesar (Andy Serkis), the chimpanzee leader of the apes, is in the trees of Muir Woods, north of San Francisco, with his fellow simians. His lieutenant Koba (Toby Kebbell) keeps an eye out, then alerts Caesar (through sign language) when a large herd of deer comes stampeding through the forest. The apes run after them for the hunt, trapping some of them. Caesar's son Blue Eyes (Nick Thurston) goes after a wounded deer, but is suddenly attacked by a bear. Blue Eyes gets wounded as the bear claws his chest, and Caesar jumps in to help his son. Caesar is outmatched and calls for Koba. Koba jumps onto the bear and kills it with his spear. Caesar thanks Koba for his help and tells his son to think before he acts.
The apes return to their sanctuary in the Muir Woods. They have established homes and even an educational system led by Caesar's trusted orangutan friend Maurice (Karin Konoval). Caesar goes to his home to tend to his sick wife Cornelia (Judy Greer). She gives birth to a baby ape. Caesar brings Blue Eyes forth to meet his new brother. Afterwards, Caesar finds Maurice, telling him that he is amazed by how far they have come as a group over the years. Maurice asks him if he still thinks of humans. Caesar admits that sometimes he does.
Blue Eyes and his friend Ash (Larramie Doc Shaw), son of Rocket (Terry Notary), are walking through the woods when a human named Carver (Kirk Acevedo) encounters them. Carver draws his gun defensively, and he shoots Ash. The gunshot alerts the other apes, as well as the humans that Carver is traveling with, led by a man named Malcolm (Jason Clarke). The apes run through the woods to confront the humans. Caesar commands them to go. Malcolm's son Alexander (Kodi Smit-McPhee) drops his bag and is forced to leave it behind.
Caesar sends Koba and two other chimps to follow the humans.
Malcolm and the humans return to their area in the ruins of San Francisco, reporting to their leader Dreyfus (Gary Oldman) on the group of apes and Caesar's ability to speak. The humans' goal is to gain access to a nearby hydroelectric dam and activate it in order to supply their community with enough limited power to last them for a little while longer. Meanwhile, Caesar gathers his apes and rides into the city on their horses to face the humans. Caesar declares that the apes do not want war, but they will fight back if they must. They also return Alex's bag to him, and Caesar tells the humans to never return to their forest sanctuary.
Dreyfus addresses the humans, riling them up and fueling their distrust for the apes and their anger for what has happened. He speaks to Malcolm afterwards, who tells Dreyfus that if he is given enough time, he can convince the apes to let him get to the dam and take out the blockage to generate power. Dreyfus agrees and gives Malcolm three days to complete this task. Malcolm prepares himself to go out with a few humans. His wife Ellie (Keri Russell), a nurse, volunteers to go with him, but he wants her to stay home with Alex. Alex overhears and decides to join his father.
Malcolm and his group travel back to the woods, leaving him to enter the sanctuary by himself. He is captured by gorillas and taken before Caesar. Malcolm explains that he means no harm and only wants to get to the dam. He shows Caesar and the apes the facility with the power systems to prove it to them. Caesar allows Malcolm to carry through with the task, but first he and the others must hand over their guns. The apes break the guns apart. Koba approaches Caesar and expresses his distrust for humans, having been experimented on in the Gen-Sys labs, leaving him with multiple scars. He also doesn't seem to approve of Caesar's affection for the humans. Caesar, however, sees this as a chance to make peace with the humans.
The humans set up a camp in the woods. One human, Foster (Jon Eyez), points out that what makes the apes stronger is that they don't require power in the same way that humans do, since they can adapt to their surroundings more easily. Carver also addresses Malcolm and Ellie, as they have each lost someone close to them from the virus (Malcolm's first wife and Ellie's daughter).
Caesar and the other apes prepare for another hunt, but Koba is nowhere to be found. He has taken two other apes into the city where they come across the humans in their compound using their firearms, essentially discovering their supply of weapons to use against the apes. Koba comes across two men, pretending to be a playful chimp, blowing raspberries and hooting. The two men order him to leave, still seeing him as a threat. Koba turns and leaves, his characteristic snarl returning to his face.
Malcolm, Carver, and Foster work in the dam to remove the blockage. They successfully blow it out but the blast temporarily traps them. Carver's leg is also wounded. Ellie is able to convince the apes to help dig the humans out of the rubble. They return to camp for Ellie to treat him, while some apes, including Caesar, come by. Caesar's baby son goes over to the humans. Ellie and Alex immediately take a shine to him, finding him adorable. Carver is less welcoming. When the little ape comes over to a box containing a gun, Carver reacts on instinct and seizes the weapon, aiming it at the apes. Caesar grabs the gun from him and whacks him with it, furious. Malcolm calms Caesar down, and the ape throws the gun into the river. He orders the humans to leave. However, Malcolm and Ellie find Caesar as he tends to Cornelia, who is very sick and weak. Ellie offers to aid her with their antibiotics. Caesar gives them one day to stay to help his wife. Foster forcefully takes Carver back to the truck and leaves him there, taking the truck's keys so Carver can't run off.
The humans return to the dam to finish their job. Koba comes back after warning the other apes of the humans' weapons supply and nearly attacks Alex. Malcolm protects him, but Maurice steps in and defends both humans. Koba angrily tells Caesar that he believes Caesar loves the humans more than he does the apes. Enraged, Caesar attacks Koba, beating his face until he decides he cannot kill him -- one of the apes' guiding principles, seen on Maurice's teaching wall is that no ape will ever kill another ape. Koba extends his hand to Caesar for forgiveness. Caesar accepts.
Koba returns to the compound to find the same two men sharing a drink. He once again plays up the silly chimp act, entertaining the two men. They hand him their bottle for Koba to drink from, but he spits it out. With their attention diverted, Koba grabs one of their rifles and kills the two men. He leaves with the rifle, then later finds Carver sitting in the van. Koba pulls him out through the window and beats him to death.
By nightfall, Malcolm and his group have successfully reactivated the generator and are able to play music. Caesar guides Malcolm and the others to a higher level to show them the lights going up in the city. Cornelia has also gotten better. Just when everything looks fine, Koba appears with the rifle. Only Caesar sees him mere seconds before Koba shoots him. Caesar falls from the tree to the ground. Koba flees, leaving only the rifle and Carver's cap, which Blue Eyes comes across. Maurice tells Malcolm, Ellie, and Alex to run as the other apes become frightened and wild. Koba convinces them all that humans have shot and killed Caesar. He rounds up all the males and charges into the city, as Malcolm and his family are forced to hide.
The humans are celebrating the return of their power by dancing. Dreyfus retreats to his private quarters to check his iPad and see pictures of his wife and two sons, who have since been lost to the virus. He breaks down into tears at the sight of them. He then goes to the control room where another man is trying to get contact through the radio. Suddenly, Koba and his gorilla/chimp army ride into the compound to lay siege to the humans. Dreyfus gathers a group of armed men to stand over the gates to fire at the apes. He grabs a rocket launcher and manages to hit several targets, killing a few apes. Koba manages to charge with his apes through the gates and break their wall down.
By daybreak, Koba and his followers have taken humans as prisoners, declaring that they now know what it feels like to be caged. They find two humans, one of which is swinging a post at the apes, which Koba grabs from him. He orders Ash to use it on the man, but Ash shows mercy and says Caesar wouldn't want this. In response, Koba grabs Ash and drags him to a balcony and hurls him over to his death. Meanwhile, Malcolm and his family find Caesar, alive but weakened. They take him away and he leads them to his old home where he was raised by humans. They begin to try and treat his wounds, just as the apes run through the city, now armed with the humans' guns. The apes that refused to follow Koba have been locked in a bus. Blue Eyes sees Maurice, who tells him to protect himself.
Ellie wants to operate on Caesar but needs medical supplies. Malcolm offers to go back to the city via the subway system and get the supplies, narrowly escaping being killed by apes with machine guns. He eventually hides in a room, only to encounter Blue Eyes, who holds his gun up to Malcolm, but cannot bring himself to shoot him. Malcolm tells him that his father is still alive, leading him to Caesar. Blue Eyes sees the bullet wound and growls at the humans, but Caesar tells him this was Koba's doing. Blue Eyes tells his father that his mother and brother are safe for now, but Koba is amassing more followers due to their fear, and he also tells Caesar that Koba killed Ash, causing Blue Eyes to weep.
At night, Caesar goes to the attic and finds an old camera with a video of him as a young chimp with his human owner, the late Will Rodman (James Franco in archive footage), teaching him. Malcolm comes up and asks Caesar who that is. He responds that he was a good man, just like Malcolm.
Maurice and the other trapped apes break free from their bus and break the humans out. They find Caesar and tell them about Koba's plan to get the female apes and young ones to join him, including Cornelia and their newborn. Together, along with Malcolm, they head out to stop Koba.
Koba and his followers have gathered at the top of a tower, while Dreyfus and two other men have recently made contact with the military and loaded the tower with C4 explosives to take the apes down. While Caesar and his friends go to face Koba, Malcolm encounters Dreyfus and the men, and draws his rifle to stop them and convince them not to go to war with the apes. Dreyfus refuses to relent, saying he is about to save the human race. He grabs the detonator and pushes the button, causing an explosion that kills him and the two men, as well as any apes within the tower, but Malcolm escapes the blast. At the top of the tower, Caesar comes face-to-face with Koba, still wielding his rifle. Koba once again tries to rally the apes, claiming that together, they are strong. Caesar fights his former ally, while the other apes stand by for Caesar. In the chaos, Koba takes his gun back and begins to shoot at the apes. Caesar dives in and tackles Koba, knocking him off a ledge. As he hangs on for his life, he looks up at Caesar, who pulls Koba's arm up. Koba tells him, "Ape not kill ape." Caesar looks him down and replies, "You are not ape." With that, he drops Koba and allows him to fall to his death.
The free and surviving apes, including Caesar's family, come up to the tower to reunite as a group. Malcolm goes up to find Caesar and warn him about the incoming military reinforcements that would threaten his family and start a war. Caesar says that an ape has already started a war, and that Malcolm must go and protect his own family. The two of them acknowledge their friendship, but also the fact that the chance for peace is gone. Malcolm slips away, leaving Caesar to stand over the apes, who all bow down to him once again.
At the end of the closing credits, the sound of howling apes and the scraping of rubble can be heard.