Plot
Time-displaced astronaut Taylor and the mute Nova travel through the desert of the Forbidden Zone in search of a new life away from Ape City. Without warning, fire shoots up from the ground and chasms open. Confused by this, Taylor investigates a cliff wall and disappears through it. Unable to reach him, Nova is left alone.
After being sent to search for Taylor and his crew, a second spaceship crash-lands on the Forbidden Zone. Brent, the only survivor, notes he is in the year 3955, but assumes he has travelled to another planet. After burying his fellow astronaut Skipper, he encounters Nova and notices she is wearing Taylor's dog tags. Hoping Taylor is still alive, he rides with her to Ape City and is shocked to discover the simian civilization. The gorilla General Ursus leads a rally for the apes to conquer the Forbidden Zone and use it as a potential food source, against the objections of the orangutan Dr. Zaius. Brent is wounded by a gorilla soldier and taken by Nova to the home of the chimpanzees Cornelius and Zira, who treat his wound and mention their time with Taylor.
Attempting to flee the city, Brent and Nova are captured by gorillas. Ursus orders they be used for target practice, but Zira helps them escape. They hide in a cave that turns out to be the ruins of the Queensboro Plaza station of the New York City Subway. Brent realizes he is in Earth's post-apocalyptic future. Upon hearing a humming sound deeper into the tunnels, Brent becomes agitated and erratic and attempts to kill Nova, before stopping and backing away to another room. Entering the remains of St. Patrick's Cathedral, he finds a population of telepathic humans who worship an ancient nuclear bomb.
Brent and Nova are captured and interrogated by the telepaths, who are descendants of the human survivors of a nuclear holocaust. They mutated over generations and claim to be a peaceful society, despite using mind-control and illusion on their enemies. The mutants force Brent into revealing the apes' march on the Forbidden Zone. Their attempts to repel the invaders with illusions of fire and other horrors fail, as Zaius sees through them. With the apes closing in, the telepaths plan to detonate their "Divine Bomb" as a last resort, holding a religious ritual. During the ritual, the telepaths remove their human masks to reveal disfigurements of sickly pale skin, scarring and vascular varicose disease.
Brent is separated from Nova and taken to a cell where he finds Taylor. One mutant, explaining that they cannot let them leave the city alive for fear of revealing it to the apes, uses his telepathic powers to force Brent and Taylor to fight each other. Nova escapes her guard and runs to the cell, screaming her first spoken word: "Taylor!" This breaks the mutant's concentration, freeing the astronauts from his control long enough for them to kill him. Taylor recognizes the bomb's insignia "ΑΩ" as a "doomsday bomb", which has a cobalt casing capable of igniting the atmosphere and incinerating the entire planet.
The apes invade the subterranean city, making their way to the cathedral; many mutants are either captured, killed, or die by suicide. After Nova is killed by a gorilla in the midst of the chaos, Taylor and Brent reach the cathedral as Mendez, the telepaths' leader, is shot dead after raising the bomb into activation position. The humans attempt to stop Ursus from accidentally setting off the weapon, but Taylor is shot in the chest while pleading to Zaius. Zaius refuses to listen and decries humanity's violence and the ruination of all things, unaware that his own apes are doing the same thing. When Brent is gunned down after killing Ursus, the mortally wounded Taylor curses Zaius, collapses and dies, bringing his hand down on the bomb's detonation switch. The bomb goes off, destroying the entire planet.