In the wake of the Simian Flu pandemic, which decimated nearly 99% of humanity, survivors now navigate a perilous existence, forming a primitive society amidst the ruins of civilization. Tragically, this catastrophe has given rise to a new order among the simians, as the virus endows them with heightened intelligence. Guided by Caesar (Andy Serkis), the apes have established a flourishing colony in the stunning Muir Woods National Monument, located near San Francisco. They are supported by three loyal lieutenants: Maurice, Rocket, and Koba.
As the remnants of humanity strive to rebuild their lives, a faction of survivors led by Malcolm (Jason Clarke) embarks on a journey into ape territory, aiming to locate a hydroelectric dam to restore power to their beleaguered community in the city. Unknown to them, this intrusion sets off a series of events that will have profound consequences. A chance encounter between Carver and Rocket's young son, Ash, ignites a tense situation, but Malcolm's quick wits help to defuse matters temporarily. However, Caesar, prioritizing the safety of his colony, commands the humans to leave.
Fueled by Koba's insidious motivations, Caesar reluctantly assembles an army to assert his dominance, demanding the humans respect boundaries. Seizing this moment, Malcolm courageously negotiates with Dreyfus (Gary Oldman), the leader of the human survivors, persuading him to send a small contingent into the forest, where Malcolm hopes to establish peace and gain access to the dam. After a precarious standoff, Caesar permits them to work on the generator with the stipulation that they relinquish their weapons.
As humans and apes join forces on this crucial mission, Malcolm's wife, Ellie (Keri Russell), and their son, Alexander, unexpectedly connect with their primate allies. However, the delicate peace is jeopardized when a hidden gun belonging to Carver is revealed, compelling Caesar to expel him from the colony. Trust is ultimately restored when Ellie risks her own safety to rescue Cornelia, Caesar's ailing spouse, showcasing the potential for empathy beyond species.
On the other hand, Dreyfus demonstrates a proactive stance by arming his community with weapons from the Fort Point armory. This decision incites skepticism in Koba, who harbors a profound animosity towards humans due to his traumatic experiences as a lab experiment. Tension escalates when Koba confronts Caesar, accusing him of prioritizing human welfare over that of their own kind. In a fierce showdown, Caesar bests Koba without taking his life.
Enraged by humiliation, Koba orchestrates a revenge plot, murdering two guards at the armory, stealing a gun, and subsequently killing Carver. Under the guise of a festive gathering, Koba cunningly ignites chaos by incinerating the ape settlement. While the colony is engulfed in turmoil, he seizes the opportunity to strike Caesar with a seemingly lethal blow, framing the humans for the ensuing attack in a bid to ignite conflict and gain control over the ape army.
Koba's devious plans lead to a full-scale assault on the human settlement in San Francisco, where his forces wreak havoc and secure the armory. Despite suffering numerous casualties, the apes capture the humans, with Dreyfus making a hasty escape. Koba also revels in the brutal execution of Ash, who bravely resisted his evil ambitions, and imprisons Caesar's loyal followers, including Rocket, Maurice, and Luca.
Meanwhile, Malcolm's family finds Caesar gravely wounded and rush him back to their old home in San Francisco. After a secretive return to gather supplies, Malcolm crosses paths with Blue Eyes, Caesar’s young offspring. Initially distrustful, Blue Eyes eventually spares Malcolm, leading to an emotional journey to find his father. When they reunite, Malcolm reveals the good news about Caesar’s survival, allowing Blue Eyes to reconnect with his father.
Together, they return to liberate the imprisoned humans and apes. Upon rescuing their former captors, Malcolm discovers Dreyfus rigging the base of a tower with explosives, having established contact with a military base. The human leader lays out a desperate plan to confront Koba atop the tower.
In a last-ditch effort to rid the world of apes, Dreyfus detonates explosives, sacrificing himself in the chaos. With the ensuing dust settled, Caesar must confront Koba, choosing not to intervene as his former ally tumbles to his demise.
As the threat of humanity's retaliation looms ominously, Malcolm rushes to deliver a critical warning to Caesar: the armies of men are only hours away from unleashing chaos upon the ape stronghold. Fearing that this brutal assault may irreparably mar the chances for coexistence, Caesar demands that Malcolm quickly take his family to safety away from the impending slaughter. As the apes prepare for war, their leader steps forward to rally them with a powerful address, bracing them for the brutal confrontations that lie ahead.
