As the shadow of disaster looms over their home planet, a determined trio of chimpanzees—Cornelius, Zira, and Dr. Milo—seize the chance to salvage and restore the spacecraft belonging to the brave astronaut Taylor. The explosive shockwave from Earth's impending cataclysm propels their vessel through time, landing them unexpectedly in 1973, right on the sun-drenched Pacific coast of the United States.
Their sudden presence at the Los Angeles Zoo ignites a wave of curiosity among scientists, capturing the attention of Drs. Stephanie Branton and Lewis Dixon, enthusiastic researchers keen to learn from their extraordinary new acquaintances. Tragedy strikes, however, when Dr. Milo falls victim to an aggressive gorilla, a loss that leaves the chimps vulnerable.
As news of the spaceship and its unusual inhabitants spreads rapidly, a Presidential Commission is formed to explore the enigma surrounding Taylor's ship and its unusual crew. Although Cornelius and Zira initially withhold details about their connection to Taylor, they ultimately disclose their origins from a war-torn future where humanity has nearly annihilated itself.
In the face of newfound fame, the apes tread cautiously, aware that their existence in 1973 poses a significant risk. They confide in Stephanie and Lewis about the grim future that looms for humanity, including the catastrophic ruin of their world. Left in disbelief, the scientists realize the necessity of keeping this knowledge concealed, at least until they better understand how society might react.
While enjoying their moment of celebrity, the apes attract the interest of Dr. Otto Hasslein, the President's Science Advisor, who becomes fixated on Zira’s pregnancy and the secrets behind their extraordinary evolution. Cornelius warns that human destructive tendencies will lead to their ultimate demise, with Zira revealing that the war was ignited by gorillas while chimps were mere victims.
Suspicion mounts when Zira inadvertently reveals her background as a human dissectionist during a critical congressional hearing. This confession unravels a series of events that leads Lewis to administer a truth serum to Zira while Cornelius is detained. As the serum takes effect, Hasslein uncovers chilling revelations about Zira's past and her knowledge of Taylor’s identity.
Facing political pressure, the President reluctantly approves Zira’s termination and sterilization, putting both she and Cornelius in grave danger. As fear grips them, they brace for the fallout from Hasslein's investigations, which he plans to exploit to legitimize their execution. Tensions rise when Cornelius lashes out at an orderly, leading to unforeseen tragedy.
Hasslein seizes this opportunity to call for the apes’ capture, but the President insists on due process. Branton and Dixon intervene to save the apes, relocating them to Señor Armando's circus, where they find temporary refuge. Just as Zira goes into labor and names her child Milo in honor of their deceased friend, the threat of capture escalates.
Determined to secure the apes, Hasslein enacts a comprehensive search for them, compelling Armando to insist on their immediate departure for safety. Lewis arranges for the chimps to hide out in the Los Angeles harbor, providing Cornelius with a pistol, aware that assassination is imminent if they are discovered. Chaos erupts as Hasslein tracks them down—you see that Zira sustains fatal injuries, and her child is slaughtered in the fray.
In the heat of battle, Cornelius retaliates and fatally wounds Hasslein, only to fall victim to a sniper's bullet himself. Zira, clutching her deceased son, attempts to escape, while Lewis and Stephanie witness the devastating events unfold. In a poignant twist, Zira had surreptitiously swapped her child with Heloise’s, a secret known only to Armando. As he prepares to move to Florida, they are met with an astonishing revelation: Milo speaks for the first time, signaling a pivotal change in the apes' fraught ordeal.
