Cornelius and Dr. Milo are thrown into a pit inside the cavern of a mountain by mutant apes. The nearby Ape village, where the city has been getting its crops, have been keeping them a secret. The two chimps discover ancient cave drawings which seem to depict apes as slaves and another type of ape in control of them. They eventually climb out of the pit and see a pueblo-like city, inhabited by the hairless mutant apes. Then, they are mind-controlled to fight one another, like Taylor and Brett in Beneath the Planet of the Apes.
Meanwhile, in Ape City, the chimps and gorillas are not getting along. The gorillas fared better during the flood and the chimps want their help to rebuild their section of the city. Meanwhile, Zaius wants to tell the public that mutants had controlled some of the gorillas to shoot the chimps during the flood-- but his wife urges him not to share that information because it would probably cause a greater panic. And Zira continues to raise her young nephew, Lucius, whose parents were killed in the recent flood.
The story definitely goes in a surprising direction and continues to set up an interesting back story for the original series. It takes place eight years before Taylor and his crew crash land in the Forbidden Zone.