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Ten years after a worldwide series of ape revolutions and a brutal nuclear war among humans, Caesar must protect survivors of both species from an insidious human cult and a militant ape faction alike.

After conquering the oppressive humans in "Conquest for the Planet of the Apes", Caesar must now keep the peace among the humans and apes. Gorilla General Aldo views things differently, and tries to cause an ape civil war. In the meantime, other human survivors learn of the ape city, and decide they want to take back civilization for themselves, thus setting the stage of warring ape factions and humans.—Humberto Amador

The orangutan Lawgiver, in "North America - 2670 A.D.", explains to an unseen audience some key events of ape and human events in the late 20th century, then moves forward to the story of the chimpanzee Caesar in the early 21st century, years after a global nuclear war has destroyed human civilization.

Living with his wife, Lisa and their son, Cornelius, Caesar creates a new society while trying to cultivate peace between the apes and remaining humans. Caesar is opposed by an aggressive gorilla general named Aldo, who wants to imprison the humans who freely roam Ape City while doing menial labor.

After defusing followers of Aldo who attacked a human teacher Abe for saying "No" to apes, Caesar wonders if his own parents could have taught him how to make things better. MacDonald, Caesar's human assistant reveals to Caesar that his older brother[c] told him of archived footage of Cornelius and Zira within the underground, now radioactive ruins of what is known as the Forbidden City from the last film. Caesar travels with MacDonald and his orangutan advisor Virgil to the Forbidden City to find the archives.

It is revealed that mutated and radiation-scarred humans are living within the city, under the command of Governor Kolp, the man who once captured Caesar. Caesar and his party view the recordings of his parents, learning about the future and Earth's eventual destruction before they are forced to flee when Kolp's soldiers hunt them. Fearing the mutant humans may attack Ape City, Caesar reports his discoveries. When Caesar calls MacDonald and a select group of humans to the meeting, Aldo leads the gorillas away.

Kolp's scouts find Ape City. Believing Caesar is planning to finish off all mutant humans, Kolp declares war on Ape City despite his assistant Méndez's attempt to get him to see reason. Aldo plots a coup d'állami in order for the gorillas to take control. Cornelius overhears from a nearby tree, but is critically wounded when Aldo spots him and hacks off the tree branch he is on with his sword. The next day, after a gorilla scouting pair are attacked by Kolp's men, Aldo takes advantage of a grieving Caesar's absence to have all humans corralled while looting the armory. Cornelius eventually dies from his wounds, leaving a devastated Caesar with the revelation that Cornelius was not hurt by humans.

When Kolp's ragtag force launches their attack, Caesar orders the defenders to fall back. Finding Caesar lying among dozens of fallen apes, Kolp expresses his intention to personally kill him. The apes, however, are merely feigning death and launch a counterattack that captures most of the mutant humans. Kolp and his remaining forces try to escape, only to be slaughtered by Aldo's troops once they are out in the open.

Aldo confronts Caesar about releasing the corralled local humans and orders the gorillas to kill them. When Caesar shields the humans and Aldo threatens him, Virgil, having learned the truth from MacDonald, reveals Aldo's role in Cornelius's death. Enraged with Aldo for breaking their most sacred law, "ape shall never kill ape", all the apes begin to angrily approach Aldo. Caesar pursues him up a large tree, their confrontation resulting in Aldo falling to his death.

With Caesar now realizing that apes are no different than their former human rabszolgatulajdonosok, he agrees to MacDonald's request for humans to be treated as equals, co-existing in a new society. They store their guns in the armory; Caesar and Virgil reluctantly explain to the armory's overseer, an orangutan named Mandemas, that they will still need their weapons for future conflicts and can only wait for the day when they will no longer need them.

The scene returns to the Lawgiver, saying it has now been over 600 years since Caesar's death. His audience is revealed to be a group of young humans and apes, the Lawgiver noting that their society still waits for a day when their world will no longer need weapons, while they "wait with hope". A closeup of a statue of Caesar shows a single tear falling from one eye.