Told as a flashback to the early 21st century with a wraparound sequence narrated by the orangutan Lawgiver (John Huston) in "North America - 2670 A.D.", this sequel follows the ape leader, Caesar (Roddy McDowall), years after a global nuclear war has destroyed civilization. In this post-nuclear society, Caesar tries to cultivate peace between the apes and the surviving humans. A gorilla general named Aldo (Claude Akins), however, opposes this and plots Caesar's downfall. Caesar is married to Lisa (Natalie Trundy), the female ape of the previous film, and they have a son, named Cornelius (Bobby Porter) in honor of Caesar's father.

   Caesar regrets never having known his parents until his human assistant MacDonald (Austin Stoker) tells him about film archives of his parents, where he can also learn about the future. The archives are located in the Forbidden City, now a radioactive ruin. After obtaining a geiger counter and weapons from the armory, Caesar travels with MacDonald and orangutan Virgil (Paul Williams) to the Forbidden City and sneaks in to find the archives. However, there are radiation-scarred humans still living there under the command of Governor Kolp (Severn Darden). Caesar and his party view the recordings of Cornelius and Zira and learn about the future of the world, but barely have time to study the tapes before they have to escape being captured. Caesar assembles a meeting to report his discoveries at the Forbidden City. Aldo objects when some humans show up, and he leads the gorillas away.

   A team of scouts sent by Governor Kolp return and tell him about the Ape City. Kolp considers this covert trip by Caesar an act of espionage. His assistant, Méndez (Paul Stevens), believes they did nothing wrong and should be left alone, but Governor Kolp stubbornly declares war on Ape City, mustering the humans to destroy the ape society.

   Aldo is furious that Caesar wants to co-exist peacefully with humans, and plots a coup in order to become the Ape leader himself. Cornelius overhears this while trying to catch his escaped pet squirrel in a nearby tree. Aldo spots him and hacks the tree branch down, critically injuring Cornelius. After a gorilla scouting pair is attacked by the approaching humans (though the gorillas struck the first blow in this case by killing a human scout beforehand), Aldo orders all humans to be corralled and leads the gorillas to loot the weapons' armory. Cornelius eventually dies from his wounds, leaving Caesar devastated, but not without leaving him with a warning about Aldo's coup.It is at that moment that Kolp's ragtag force launches their attack against Ape City. The initial mutant attack succeeds, forcing Caesar to order the defenders to fall back. When Kolp finds Caesar lying among dozens of apes, he threatens to kill him, but the fallen apes, who were feigning death or hiding on Caesar's orders, launch a counter-attack that captures most of the mutants. Kolp and his remaining forces are killed by Aldo's troops while attempting to retreat.

   After the battle, Aldo wants to kill the penned humans, but Caesar shields them. Aldo declares that Caesar should be killed if he shields the humans. However, Virgil reveals Aldo's responsibility for Cornelius' death and the breaking of the ape community's most sacred law ("Ape shall never kill ape"). An infuriated Caesar pursues Aldo up a large tree, resulting in Aldo falling to his death. Caesar then attempts to free the humans, but they refuse to leave the pen unless humans are treated as equals. Caesar then realizes the apes are just as despicable as the former slave-owners, and the apes and humans then decide to coexist with one another and begin a new society.The Lawgiver finishes his wraparound narration (he says it's been over 600 years since the death of Caesar). It's revealed he's talking to a group of young humans and apes; apes and humans have continued to coexist in peace. When asked by a human child "Who knows about the future?", the Lawgiver replies "Perhaps only the dead." A closeup of a statue of Caesar shows a single tear falling from one eye.