As Taylor (James Franciscus) and Nova (Kim Hunter) traverse the arid wilderness of the Forbidden Zone in search of a new beginning, they find themselves unexpectedly threatened by a series of mysterious geological disturbances—explosive eruptions and gaping chasms that leave them both astonished. When Taylor suddenly vanishes while investigating a nearby cliff, Nova is forced to fend for herself, utterly helpless.
In a parallel storyline, Brent—the last survivor of a catastrophic spaceship crash—awakens in the year 3955, believing he is stranded on an alien planet. After laying his fellow astronaut Skipper to rest, he embarks on a quest to locate Taylor, only to stumble upon Nova, who is oddly wearing his commander's dog tags. Their encounter ignites a flicker of hope for Brent, who allies with Nova as they set out towards Ape City. However, they are met with a bewildering civilization of apes, led by the formidable General Ursus, who is fueled by a fervent desire to conquer the Forbidden Zone for its resources.
As the apes, under Ursus's command, rally for war, Dr. Zaius—an orangutan filled with wisdom and compassion—cautions against their reckless hostility. Brent’s situation takes a dire turn when he suffers an injury inflicted by a gorilla soldier and is rescued by Nova, leading them to the home of the insightful chimpanzees Cornelius and Zira, who share their troubling experiences with Taylor.
The stakes rise as Brent and Nova attempt a daring escape from Ape City but are captured and slated for execution. Just when hope seems lost, Zira intervenes, offering them a chance to flee into the depths of a forgotten subway system, once known as New York's Queensboro Plaza station. Here, Brent stumbles upon an unsettling revelation: he is not on a distant world but rather a devastated Earth, scarred by an apocalyptic event.
As he ventures deeper into the dark tunnels, Brent's psychological state deteriorates, leading him to lash out at Nova in a moment of anguish. Their escape becomes more frantic until they encounter a group of telepathic humans who revere an ancient nuclear warhead nestled within the ruins of St. Patrick's Cathedral. Desperate to extract vital information, these mutants, who are the remnant descendants of human survivors, use mind-bending tactics to manipulate Brent and Nova. Despite labeling themselves a peaceful society, their reliance on deception shadows their existence, especially when their attempts to ward off the encroaching apes through terrifying illusions collapse under Zaius's discerning gaze.
With apes threatening their society, the telepaths prepare for a final sacrificial act, a ritual destined to unleash their "Divine Bomb," marked with the ominous insignia of destruction. As the ritual unfolds, the truth becomes grotesquely clear: the mutants' human masks are stripped away, revealing the horrific effects of radiation—sickly pallor, scars, and other suffering afflictions.
In a turn of grotesque fate, Brent is captured and imprisoned, where he confronts Taylor (James Franciscus) yet again, only to find himself coerced into a violent showdown thanks to a mutant's mental powers. This savage encounter is interrupted when Nova escapes her captor, calling out "Taylor!" in a plea for their reunion, breaking the mutant's concentration. This fleeting moment of respite enables them to retaliate against their oppressor.
Taylor recognizes the insignia marked "ΑΩ" on the bomb as a signal of impending doom—a doomsday device that threatens to annihilate all life. As the apes invade the underground city, the mutants endure a desperate struggle, many succumbing to sheer terror or capture. In the ensuing chaos, Nova tragically falls victim to the brutality of a gorilla, leaving Taylor and Brent to confront the telepaths at the heart of their stronghold—inside the sacred cathedral. There, they find Mendez, the mutants' leader, on the precipice of detonating the Divine Bomb, blinded by fervor.
In a tense moment, Taylor begs Zaius to prevent planetary annihilation but is met with violence. The grim actions of the apes unveil a deeper truth: the destructive tendencies of humanity have permeated every fabric of civilization. In a climactic act of vengeance, Brent confronts Ursus, while Taylor, weakened, curses Zaius, ultimately collapsing onto the bomb's detonator. Their final defiance triggers a cataclysmic explosion that irrevocably scatters the remnants of civilization across the desolate wasteland.
