Astronauts Taylor, Landon and Dodge are in deep hibernation when their spaceship crashes into a lake on an unknown planet after a light-speed voyage. They discover their fourth crew mate, Stewart, dead due to a malfunction. The three abandon their ship when it starts sinking; Taylor remains on board long enough to see that the date is November 25, 3978, two thousand and six years after their departure in 1972.
The astronauts set off through a desolate wasteland and discover an oasis in the desert, ignoring eerie scarecrow-like figures around the edge. Their clothes are stolen while they take a swim. The astronauts pursue the thieves, finding their clothes torn to shreds and their supplies pillaged as the perpetrators, a group of mute primitive humans, raid a cornfield. Taylor is shot in the throat and captured by armed gorillas, along with the primitive humans. Dodge is killed and Landon rendered unconscious in the chaos. Taylor is taken to Ape City where he is saved after a blood transfusion administered by two chimpanzees: animal psychologist Zira and surgeon Galen. However, Taylor’s throat injury renders him temporarily unable to speak.
Taylor is placed with one of the captive primitive humans, whom he later names Nova. He observes the enhanced society of talking apes and in a strict caste system: the gorillas serving as military forces and labourers; the orangutans overseeing the affairs of government and religion; and intellectual chimpanzees being mostly scientists and doctors. While their society is a theocracy similar to the beginnings of the human Industrial Era, the apes consider the primitive humans as vermin. Humans are hunted, either killed outright, enslaved, or used in scientific experiments. Taylor convinces Zira of his intelligence as she and her fiancé Cornelius, an archaeologist, take an interest in him. Dr. Zaius, their orangutan superior, learns of this and arranges for Taylor to be castrated. Taylor escapes and finds Dodge’s stuffed corpse on display in a museum. When Taylor is recaptured, he suddenly regains his speaking abilities and much to the amazement of the onlookers, he shouts: “Take your stinking paws off me, you damn dirty ape!”
A hearing to determine Taylor’s origins is convened. Taylor mentions his two comrades, learning that Landon was subjected to a lobotomy that has rendered him catatonic and unable to speak. Believing Taylor to be of a human tribe from beyond their borders, Zaius privately threatens to castrate and lobotomize Taylor for the truth about where he came from. With help from Zira’s nephew Lucius, Zira and Cornelius free Taylor and Nova and take them to the Forbidden Zone, a taboo region outside Ape City where Taylor’s ship crashed that has been ruled out of bounds for centuries by ape law. While Cornelius and Zira are intent to gather proof of an earlier non-simian civilization which the former came upon a year before to be cleared of heresy, Taylor is more focused on the evolution of the ape world and to prove he is not of that world.
Arriving at the cave, Cornelius is intercepted by Zaius and his soldiers, with Taylor holding them off while threatening to shoot. Zaius agrees to enter the cave to disprove their theories and to avoid physical harm to Cornelius and Zira. Inside, Cornelius displays the remnants of a technologically advanced human society pre-dating simian history. Taylor identifies artifacts such as dentures, eyeglasses, a heart valve, and to the apes’ astonishment, a talking children’s doll. Zaius admits to Taylor that he always knew of the ancient human civilization. Taylor nonetheless thinks it best to search for answers, despite being warned that he may not like what he finds. Once Taylor and Nova ride off, Dr. Zaius has the gorillas lay explosives to seal off the cave and destroy the evidence while charging Zira, Cornelius and Lucius with heresy.
Taylor and Nova follow the shoreline and discover the remains of the Statue of Liberty, revealing that this “alien” planet is actually Earth long after a nuclear war. Realizing what Zaius meant earlier, Taylor falls to his knees in despair and condemns humanity for destroying the world.