Brent is the copilot of a rescue mission, sent after Colonel Taylor's ship was determined to have gone awry, in its flight to another star. Brent's ship follows the same trajectory, and runs into the same problems, crash-landing in the Forbidden Zone, only this time on land. His pilot, Colonel Maddox, is blinded, and suffers fatal injuries, dying soon after the crash.
Bewildered by events, Brent tries to make his way through the arid desert, wondering if Taylor underwent a similar fate. It turns out he's closer to meeting Taylor than he could have imagined, as he comes across a woman on horseback – Taylor's companion Nova, alone since Taylor disappeared. Discovering Nova is mute, but wearing Taylor's dog tags, he climbs onto the horse also, demanding she take him to Taylor.
Not knowing what else to do, and unable to explain Taylor's absence, Nova takes Brent to Ape City, to look for Zira. Brent overhears an anti-human speech by General Ursus, and his mind reels with mounting horror at the place he's come to: "If this place has a name, it's the Planet Nightmare!" Wounded by a gorilla soldier, Brent takes refuge with Nova at the home of Zira and Cornelius.
Cornelius and Zira (who tends to Brent's wound) help Brent and Nova get out of Ape City, but gorilla soldiers follow them into the Forbidden Zone. Hiding in a cave, they discover an old subway tunnel, and follow it deep underground to the ruins of New York City, and its mutant inhabitants. Brent is tested by the mutants, through their psychic abilities, forcing him to try to kill Nova, and to go where they want him. They interrogate him telepathically.
After Brent and Nova witness a mutant religious service (where mutants both worship an unexploded doomsday bomb, and reveal themselves to be hideously disfigured, from lingering radiation inside the zone), Brent is reunited with Taylor, who was taken prisoner. Their pleasure at meeting each other is broken by the sudden realisation of the mutants' final plans for them both; as their jailer explains: "We don't kill our enemies. We get our enemies to kill each other." Taylor and Brent are then forced by the jailer's mental powers to fight one another.
Nova, who was separated from Brent after the worship service, gets loose from her guard, and finds Taylor and Brent fighting to the death. She is so stirred by the sight that she speaks for the first time in her life, crying "Taylor!" and bringing the fight to a sudden stop. The jailer's concentration broken, Brent and Taylor act, killing him but inadvertently locking themselves in the cell with Nova.
The three break the cell's lock just as the gorilla army invades the underground city. A random shot kills Nova, demoralising Taylor, but Brent urges him to join the oncoming fight. Hurrying to the cathedral, Brent and Taylor take rifles and try to stop the apes from setting off the bomb and destroying everything. After killing General Ursus and several of his soldiers, Brent runs out of ammunition, and he is killed by the gorilla troops. A moment later the bomb detonates, triggered by Taylor as he falls in death, and Earth is destroyed.