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Ten years after the global pandemic of a deadly Simian Flu,[a] the worldwide human population has been drastically reduced, with only about one in 500 genetically immune. Civilization is destroyed as a result of societal collapse. The apes, under the chimpanzee Caesar, all bestowed with genetically enhanced intelligence by the virus, have long-established a colony in the Muir Woods near San Francisco.

A group of humans, led by a man named Malcolm, trespass the apes' territory from San Francisco in search of a hydroelectric dam that would restore power to the city. An encounter by Caesar's son Blue Eyes and his friend Ash leads to the latter's injury by a man named Carver. Malcolm manages to prevent further escalation, and Caesar orders the humans to leave. Prompted by Koba, a scarred bonobo with a vendetta against humans for his mistreatment as a laboratory test subject, Caesar brings his army to the humans' community as a display of strength.