Will Rodman, a scientist at the San Francisco biotech company Gen-Sys, is testing the viral-based drug ALZ-112 on chimpanzees to find a cure for Alzheimer's disease. ALZ-112 is given to a chimp named Bright Eyes, greatly increasing her intelligence. But then, during Will's presentation for the drug, Bright Eyes is forced from her cage, goes on a rampage, and is shot to death. Will's boss Steven Jacobs terminates the project and has the chimps slaughtered. However, Will's assistant Robert Franklin discovers that the reason for Bright Eyes' rampage was that she had recently given birth to an infant chimp. Will reluctantly agrees to take in the chimp, who is named Caesar. Will learns that Caesar has inherited his mother's intelligence and decides to raise him. Three years later, Will introduces Caesar to the redwood forest at Muir Woods National Monument. Meanwhile, Will treats his dementia-suffering father Charles with ALZ-112, which seems to restore his cognitive ability.

Five years later, when Caesar reaches adolescence and sees a dog on a leash like his own, he questions his identity and learns of his origins from Will. Meanwhile, Charles's condition returns as he becomes resistant to ALZ-112. Caesar injures a neighbor, Douglas Hunsiker, while defending a confused Charles. As a result, he is placed in a primate shelter where he is tormented by a chimp named Rocket and the chief guard, Dodge Landon, but also where he befriends an orangutan named Maurice who came from a circus. Caesar learns how to unlock his cage, gaining free access to the common area. With the assistance of a gorilla named Buck, he confronts the sanctuary's alpha, Rocket and claims that position. Meanwhile, Jacobs clears development of a more powerful, gaseous version of the drug – ALZ-113 – when Will tells him it can also improve intelligence. Will takes the drug home to try to save his father, but Charles declines further treatment and dies overnight.

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