Two astronauts survive a crash-landing on a planet where intelligent apes rule over humans. The men find that their own intelligence challenges the apes' superiority and puts their lives in danger.

Burke and Virdon are faced with having to fight to the death when they are captured, and the Ape Prefect amuses himself by staging gladiator-style fights between the humans in his charge.

When they are buried alive, underground, in an ancient San Francisco subway station during an earthquake, Burke and General Urko are forced to work together. Above ground, Galen and Virdon try to figure out a way to help Burke, with the assistance of several gorilla soldiers.

When Galen hurts his leg and can't travel, Virdon and Burke seek refuge in a farm till their friend recovers. The farm is operated by a gruff but decent ape named Polar, his wife Zantes, and their three children: older son Anto, younger son Remus, and daughter Jillia. Polar puts to work the two strangers who teach him about contour farming, windmill building, seed selection, etc.

Burke and Virdon discover a holographic message from scientists from their own time, which might help them find out what happened to their world, while they are exploring the ruins of Oakland.

While walking on an ocean beach with Galen, Virdon and Burke see a condemned man lashed to a raft in the water. They rescue him and carry him to a nearby cave but then an ape-on-patrol captures the two astronauts and takes them to his boss, Hurton. Hurton administers a fishing operation and he presses Virdon and Burke into service as fishermen after they pass a test by swimming under a sheet of flames.

Galen risks his freedom, and life by contacting his old sweetheart, Kira, when Virdon is seriously injured. Kira is now a talented, and forward thinking, surgeon; and Galen shares with her a forbidden book on human anatomy, that he and Burke stole from Dr. Zaius' home, with her.

Galen, Virdon and Burke befriend a chimpanzee named Fauna, the blind daughter of a human friendly ape who was killed by a band of vigilante apes known as the Dragoons. Unaware that Burke is human, Fauna falls in love with him, as Galen and Virdon hunt down the Dragoons, only to discover that Fauna's uncle is one of them.

Virdon agrees to race a chimpanzee Prefect's horse against Urkos best horse, in exchange for a condemned boy's freedom. Urko has never lost a race, but of course, as Virdon finds out, Urko doesn't play fair. Despite Urko's treachery and cheating, Virdon prevails in the end.

When Burke is captured by Urko's soldiers, he is forced to face two equally horrifying options: he can either be killed, outright, by Urko; or he can be used in a brainwashing experiment, being performed by a prominent ape doctor, using a forbidden (human) text on the subject.

To foil the plans of a tyrannical gorilla who is trying to overthrow the chimpanzee prefect and gain control over a human farming district, Galen, Virdon and Burke risk an encounter with Urko. Urko and Burke are forced to work together again.

With the help of an ape doctor, Virdon and Burke race to concoct a cure for a malaria outbreak. They must succeed before Urko implements his own version of a cure: burning down the village with everyone in it.

When they are captured by a human community that provides human slaves to the apes, Virdon and Burke's survival is dependent on convincing their captors to rebel against the apes.

Unaware that a chimpanzee scientist plans to use a human prisoner's flying machine for her own deadly purpose, Virdon, Burke and Galen help the man, Leuric, to build a hang glider.