Civilization of the Planet of the Apes is a suggested sequel idea to Rise of the Planet of the Apes. Because the real canon sequel does not have a script yet, here's a suggested sequel, typed in to mostly fit in properly by tone and story wise.
Picking off three weeks after where the ALZ-113 spread across the world, human civilization has been entirely affected with 5.7 billion deaths. With no where on Earth secure from the ALZ-113, the humans are now living underground to hide themselves from the ALZ-113 virus. There were highly desperate attempts to dig very deep into the dirt or hiding in the sewers. The humans are then suffering from the lack of oxygen, food, and fresh water underground. Because of this, the humans start wearing gas masks at all costs and started returning back above the underground.
Meanwhile, Caesar, Maurice, Rocket, Cornelia, and several other chimps, orangutans, bonobos, and gorillas are living in the Muir Woods Park and there are the first newborn apes. In fact, Caesar had freed several apes stuck in every zoo near San Francisco and there are much more apes living in the park. Caesar is in charge of the Muir Woods Park ape society, and because the apes are becoming more intelligent, they are becoming more like humans. The apes are now almost completely bored with having to live in the Muir Woods Park since they are desiring lives that are more complex while Caesar, Maurice, Rocket, and Cornelia are still happily satisfied with living in the forest. The apes are unable to create original blueprints to construct houses or tools. Caesar suggests that abandoning the project is necessary since he found technology to be only important to humans.
Koba, the bonobo who has an incredible hatred towards humans, encourages most of the ape population to follow him into the ghost city of what was known as Sacramento. The apes who have followed Koba are confused on why he brought them to a ghost city where humans once lived. Koba demonstrates to the apes on how to use technology that humans have invented. Koba knows very much since he was experimented on with the ALZ-113 several times and has become highly intelligent. The apes begin by sleeping in beds that have pillows, sheets, and covers, discovering and consuming more sophisticated types of food, learning how to turn on lamps and lights, and learning how to tell time. The apes who have been led by Koba are now more satisfied with living in the towns that humans once lived in rather than in the Muir Woods Park.
Caesar is disappointed to realize that most of the apes have left the society he established in the Muir Woods Park and the only apes who still remain with him are the rebellious warriors who participated in Rise in fighting the human authorities before reaching the forest. Maurice suggests that they follow where most of the apes have went, wondering what their lives are like now.
Koba is now teaching the apes how to read and write, as demonstrated he is literate from Rise, again because that he was experimented on several times with the ALZ-113. The apes are learning English because it is the language that is the most available to learn from the texts that the humans have left behind. Koba is pleased to learn that the ape society is while much more intelligent, still eager to become smarter and better. Koba takes them to learning much more, developing bigger plans, enthusiastic that a smarter ape society will mean a better ape society.
Caesar and his loyal followers including Maurice arrive at the ghost city that Koba and the apes are currently living in. Maurice spots that he has found a chimpanzee trying to use a human computer at a library, with Caesar seriously observing. Once the chimpanzee leaves, Caesar finds on the screen the words "All Hail Koba" on it. Caesar then finds a human library where tens of apes are using computers astonished by how much the apes are advancing. Caesar asks where Koba is, but the apes respond to him that Caesar is not able to talk to Koba at the moment.
Caesar finds that Koba is inside a room talking to a group of apes. He even finds that now the apes are improving their vocal skills with only still having some problem with pronounciation.