Upon crash landing on the Planet of the Apes, John Brent and Nova encounter a group of primitive humans who worship a nuclear bomb and believe it to be a god. Brent soon learns that Taylor has disappeared into the Forbidden Zone and sets out to find him.
On his journey, Brent discovers an underground city where a race of mutant humans live. The mutants possess powerful telepathic abilities and plan to detonate the nuclear bomb to destroy all life on the planet, including the apes and themselves.
Brent manages to locate Taylor, who has been captured by the mutants and forced to take part in their plan. Together, they attempt to stop the mutant's plot and save the planet from destruction.
In a climactic finale, the mutants are ultimately unsuccessful in their plan and the nuclear bomb detonates, causing the complete destruction of the Planet of the Apes. Brent and Nova manage to escape on a spaceship, but are sent hurtling through a time vortex, leading to the events of the subsequent movie, Escape from the Planet of the Apes.