Upon releasing the water and restoring the city’s power, Koba appears and challenges Caesar to a fight claiming that “Caesar love humans more than apes!” Koba attempts to beat Caesar while Caesar takes the upper hand and Koba escapes.
Malcolm leads Caesar and his comrades Maurice, Rocket and River to the dam where the water supply is blocked. Upon returning from their mission, Koba convinces his people, and even Caesar's son River, to keep the discovery of the weapons from Caesar. Koba, who has convinced a number of apes of Caesar’s betrayal, goes rogue with a small team and spies on the human survivors only to learn that they have been supplying weapons to secretly start war with the apes. In return Caesar agrees to help Malcolm and his team to unblock the water blockage. Malcolm convinces Caesar that he can help and brings his wife Ellie, who was a nurse, who gives Cornelia an antibiotic that eventually saves her life. While upon their conversation, Caesar in summoned to his wife Cornelia who learns that she is ill and might not survive. When entering Caesar’s domain, Malcolm is captured by gorillas and taken to Caesar for judgment. Meanwhile, Malcolm and his group have set up camp at the bottom of the woods and attempts to go negotiate with Caesar in helping them breaking the water out of the blockage.
Koba, who had been experimented upon in the labs of Gen-Sys, becomes aware of Caesar’s affectionate side towards humans and begins to spread the word to the other apes. Caesar, along with his army, arrives at the human domain and tells the humans “Apes do not want war” and orders them never to come back. The apes, who have thought that human existence has long been gone, summon Caesar who sees Malcolm, realizing he is not like the humans they fought, lets the humans go through their resistance from fighting and orders them never to return. While the human group enters the woods, River and Rocket's son Ash run into the humans, lead by Malcolm and his wife Ellie followed by their son Alexander and some other survivors. Malcolm, a survivor of the ALZ-113 pandemic, convinces the human leader Dreyfus to give him three days to make peace with the apes in the hope that they will help unblock a water blockage in the woods to help bring back power to the city, before Dreyfus leads his team to kill the apes by surprise. All the struggle seems to have gone away from the past ten years, with the comfort that Caesar has a family with his wife Cornelia, his teenage son River, and his newborn son. After a struggle with a grizzly bear, Caesar is summoned to his home, in the middle of the Muir Woods, where his wife has given birth to a newborn son. Caesar leads some of his apes to a hunting party to kill some deer for food. A middle aged Caesar now leads and governs a new generation of apes, including some of his comrades from the ape sanctuary he broke out with. The film opens with a breaking news report showing the ten-year global pandemic of the ALZ-113 virus, since the ape breakout in San Francisco. They reach a fragile peace, but it proves short-lived, as both sides are brought to the brink of a war that will determine who will emerge as Earth's dominant species. A growing nation of genetically evolved apes led by Caesar is threatened by a band of human survivors of the devastating virus unleashed a decade earlier.