Many generations have passed since the fall of Caesar, leading to the establishment of various ape clans while humans have descended into a feral existence. In this world, Noa, portrayed by Owen Teague, a spirited young chimpanzee from a unique falconry-oriented clan, prepares for an important coming-of-age ceremony alongside his friends Anaya and Soona, both played by Travis Jeffery and Lydia Peckham respectively. As they embark on a quest to gather eagle eggs, disaster strikes when a human scavenger unknowingly smashes Noa's egg during a chaotic encounter. Determined to find a replacement, Noa’s journey takes a dark turn when he stumbles upon a menacing group of ape raiders armed with electric weapons.
In a desperate attempt to evade them, Noa's hiding only leads the raiders back to his own community. Upon his return, he is horrified to witness his village ablaze, as the ruthless raider leader Sylva, played by Eka Darville, brutally murders Noa's father, Koro, portrayed by Neil Sandilands, after tossing Noa from a perilous height. Left for dead among the ashes, Noa regains consciousness to find his clan captured and taken away. In a heart-wrenching moment, he buries Koro, setting forth on a perilous mission to rescue his family.
Along his journey, Noa meets Raka, a wise orangutan played by Peter Macon, who enlightens him about the teachings of Caesar. However, their path is fraught with danger as they realize they are being stalked by the same human scavenger from earlier. Raka, displaying compassion, offers her food and a blanket, endearing the scavenger whom they name Nova. To their astonishment, Nova, portrayed by Mae (also played by Freya Allan), reveals her ability to speak and shares the horrifying truth: Sylva's raiders have taken Noa’s clan to a coastside settlement that conceals an old human vault.
As they traverse a bridge toward this ominous site, they are ambushed by Sylva's gang. In the chaotic skirmish, Raka courageously saves Mae from drowning but is ultimately swept away by the torrents. Captured by the raiders, Noa and Mae find themselves prisoners within the apes' settlement where Noa reunites with his clan, only to meet Proximus Caesar, the self-appointed king played by Kevin Durand. Unbeknownst to Noa, Proximus has enslaved other clans, forcing them to unearth the secrets of the vault, which he believes holds powerful human technology.
Proximus extends an invitation to dinner, where Noa, Mae, and the human captive Trevathan, played by William H. Macy, gather to discuss the past. Proximus sees in Noa a tool that could unlock the vault, warning him that Mae might have her own ulterior motives. When confronted, Mae reveals a hidden entrance to the vault and mentions a mysterious "book" that could restore the lost ability of speech to humanity. Intrigued, Noa reluctantly agrees to assist her, hoping that together they can dismantle Proximus's regime and return his clan to safety.
The group stealthily plants explosives around the levee encircling the settlement, but their plans are interrupted when Trevathan catches them mid-act. In a shocking turn, Mae kills him to safeguard their mission. Once inside the vault, they discover a cache of weapons along with Mae's so-called "book," which turns out to be a satellite key crucial for communication. They also unearth children’s picture books that depict a world where humans, once the dominant race, kept apes confined to cages, evoking a profound realization of their past.
While attempting to exit the bunker, they are confronted by the ruthless Proximus and his warriors. In a tense standoff, one of Proximus's lieutenants, Lightning, threatens Soona's life, but Mae defends her by shooting him with a weapon she found, triggering the explosives that cause the bunker to flood. As chaos ensues, Mae escapes the settlement, while the apes manage to ascend to safety. In a fierce confrontation, Noa succumbs to Sylva’s pursuit, ultimately ensnaring and drowning him before facing Proximus in a final showdown. Rallying his clan, Noa commands their eagles to strike, culminating in Proximus’s dramatic fall off a cliff and into the sea.
With the threat vanquished, Noa’s clan returns to rebuild their life, but the story culminates in a tension-filled farewell between Noa and Mae. She confesses that she destroyed the bunker to prevent the apes from wielding weapons that should only belong to humans. This leads to a poignant dialogue, where Noa questions the implications of such beliefs, pondering whether true coexistence between their species is attainable, given Mae’s profound differences.
As Noa guides Soona to explore a telescope he salvaged, Mae embarks on her own path towards a secluded human settlement at a satellite base. There, she delivers the decipher key, igniting hope as the humans reactivate their long-dormant satellite communication systems, reaching out to the remnants of their kind across the globe.
