Deep within Mount Lam, Cornelius and Milo flee the enraged Chimp villagers from the nearby Ape village. They come across some ancient New York City ruins, such as The Midtown Tunnel and sign, then are captured by the villagers. They all flee when the mutant apes arrive. They get angry and cause frightening illusions. But the reason they run is that they have little control over their abilities and may scramble their minds.
Back on the surface, the villagers, led by Amicus, sentence them to death, including Zaius' son-in-law Vitus, because they fear Orangutans and Gorillas enslaving them, as is depicted on some ancient hieroglyphics. As they are carted off they are interrupted by several mutant apes and one of them is Chinda, Amicus' daughter. Which means these mutants are born of normal apes. They are mutated because twenty-years ago, after an earthquake, their drinking water was diverted, so some came from the Forbidden Zone.
Meanwhile, Ape City is rebuilding and Dr. Zaius proposes a new improvement initiative, promising the best jobs and most help to the Chimpanzees, who were hit the hardest. But this involves farming and the chimps don't want to be farmers. There's more dissent.
Back in Painted Valley, the villagers agree to let the trio go, and when they return to Ape City they tell Zaius that the entire valley--and its population--was destroyed in the cataclysm. This is so that the mutation isn't spread and the populace of the Valley can live in peace. They do tell Zaius about the hieroglyphics, which shows that the Orangutan overlords were overthrown by the chimps--and that isn't what Zaius needs right now to throw fuel on the fire. He tells them to keep quiet about it.