The opening titles set the film in "North America – 1991." Armando (Ricardo Montalbán) explains that in 1983 (ten years after the end of Escape from the Planet of the Apes, which was set two years ahead of its theatrical release date), a disease killed the world's cats and dogs, leaving humans with no pets. To replace them, humans began keeping apes as household pets. Realizing the apes' capacity to learn and adapt, humans train them to perform household tasks. By 1991, American culture is based on ape slave labor (just as Cornelius described would happen in the previous film). It is also suggested that the North America of the 1990s is at least partly a police state, as apes and humans are being watched at all times.
The film begins with animal trainer Fred Mason (Milburn Stone) returning from his latest safari with a horde of animals for his employer John Whipple (Lloyd Corrigan), owner of the Whipple Circus. Among them is Cheela (Ray Corrigan), a gorilla with remarkably human characteristics. Mason relates that she is the most affectionate jungle animal he has ever encountered.
Alakazam is a young and brave monkey (a macaque) who has been encouraged by all the other monkeys to become their king. After attaining the throne, he becomes rude and dictatorial, and does not believe that human beings are greater than he is. Then he tricks/forces Merlin the magician to teach him magic (reluctantly on Merlin's part, who warns Alakazam that the powers he acquires now will bring him much unhappiness later).
The film makes use of a frame tale to present three self-contained "episodes" via flashback. Jane and Tarzan's first wedding anniversary has arrived, and Jane is trying to find a suitable present for her husband, with the help of the elephant Tantor, and the gorilla Terk.
Astronauts Taylor (Charlton Heston), Landon (Robert Gunner), Dodge (Jeff Burton) and Stewart are in deep hibernation when their spaceship crashes in a lake on an unknown planet after a long near-light speed voyage, during which, due to time dilation, the crew ages only 18 months. As the ship sinks, Taylor finds Stewart dead and her body desiccated. They throw an inflatable raft from the ship and climb down into it; before departing the ship, Taylor notes that the date is November 25, AD 3978, approximately two millennia after their departure in 1972. Once ashore, Dodge performs a soil test and pronounces the soil incapable of sustaining life.
In 2029, aboard the United States Air Force space station Oberon, Leo Davidson works closely with primates who are trained for space missions. His favorite simian co-worker is a chimpanzee named Pericles. With a deadly electromagnetic storm approaching the station, a small space pod piloted by Pericles is used to probe the storm. Pericles's pod heads into the storm and disappears. Against his commanding officer's orders, Leo takes a second pod and goes in pursuit of Pericles. Entering the storm, Leo loses contact with the Oberon and crashes on a planet called Ashlar in the year 5021. He discovers that the world is ruled by humanoid apes who can speak human language and treat human beings as slaves.
Deux ans après avoir affronté les humains et Koba, César et les singes vivent reculés dans une forêt. Leur avant-poste est alors attaqué par une unité militaire pratiquement annihilée dans l'assaut et qui subit une défaite totale, rapportée par radio à leur commandant le colonel McCullough. Selon les dires d'un survivant fait prisonnier et présenté à César, cet homme sanguinaire cherche à tout prix à retrouver César pour installer la domination des hommes sur les primates : bien que ça ne fasse pas l'unanimité, César choisit d'épargner les soldats survivants et de les lui renvoyer avec un message de laisser tomber afin de clarifier les circonstances ayant amené cette situation et prévenir une montée vaine des conflits. Plus tard alors qu'ils s'occupent de leurs morts et blessés, César vient accueillir son fils aîné Yeux-Bleus et Rocket, qui reviennent d'une expédition prolongée et ont apparemment enfin trouvé la terre promise des singes, à des mois de marche de là. Le soir même, après des discussions houleuses sur la suite des événements et la crainte exprimée par Winter, un gorille albinos, la décision est prise de s'y rendre. Mais après l'échec de ses soldats, le colonel McCullough se déplace en personne avec un commando dans le refuge de César afin de le tuer. Il tue le fils aîné de César par méprise ainsi que sa compagne, Cornelia, épargnant sans le savoir leur enfant cadet, Cornelius qui s'était caché. César qui arrive juste avant son départ et constate leur mort, tente de se venger pour son acte mais échoue de peu. Tandis que la colonie a débuté son trajet vers leur futur foyer, César confie alors Cornelius à Lake, la compagne de feu son fils aîné, puis quitte les siens à leur grande surprise pour se lancer seul à la poursuite de McCullough, assoiffé de vengeance. Il est toutefois vite rattrapé et épaulé par ses plus proches amis l’orang-outan Maurice, le chimpanzé Rocket (dont le fils Ash, meilleur ami de Yeux-Bleus, fut également tué, par Koba en son temps) et le gorille Luca.
Ten years after the worldwide pandemic of the deadly ALZ-113 virus (known as the Simian Flu), human civilization is completely destroyed following martial law, civil unrest and the economic collapse of every country in the world. Over 90% of the human population has died in the pandemic, while apes with genetically enhanced intelligence have started to build a civilization of their own.
Will Rodman, a scientist at the biotechnology company Gen-Sys, is testing viral-based drug ALZ-112 on chimpanzees to find a cure for brain ailments such as Alzheimer's disease. The drug is given to a chimpanzee, Bright Eyes, greatly increasing her intelligence. However, when Will is presenting 112 to his boss and uses Bright Eyes as an example, she is forced from her cage, goes on a rampage, and is killed. Will's boss Steven Jacobs terminates the project and orders chimp handler Robert Franklin to euthanize the chimps. After doing as ordered, Franklin discovers that Bright Eyes had recently given birth and understands the reason why she was disturbed. He convinces Will to save the baby chimp's life by taking him home temporarily. Will's father Charles, who is suffering from Alzheimer's, names the chimp "Caesar", in reference to William Shakespeare's play Julius Caesar, from which he can, despite his deteriorating mental condition, cite long passages from memory. Will learns that Caesar has inherited his mother's high intelligence (the 112 virus passing to him in utero) and decides to raise him, working from home and observing his behavior in hopes that he can get the project restarted. Three years later, Will introduces Caesar to the redwood forest at Muir Woods National Monument. Meanwhile, with Charles' condition rapidly deteriorating, Will treats him with ALZ-112 and he is restored to better-than-original cognitive ability.
A native village is robbed, supposedly by natives. Before a man dies, he mentions the name "Slade". Black colouring is found on his hand so they know it is white people who did it, disguised as Africans. Tarzan arrives, remembering Slade from a year previously as a man who let three of his men die during a hunt for a rogue elephant and has a grudge against him. A woman (Angie) turns up, Sanchez' latest woman, flying one of his planes. Later she buzzes Tarzan in his canoe, and crashes the plane so now Tarzan is stuck with her as he goes after Slade. Slade has 3 men and a girlfriend with him. He knows where a diamond mine is and has got his supplies for his trip by stealing them. Tensions run high amongst his men. Kruger is an ex-Nazi and a diamond expert. O'Bannion is an Irish rebel, a drunk and a trouble maker who keeps hassling Dino till Dino decides to kill him but falls foul of a wild animal and quicksand.
Eleanor Reed (Eleanor Holm) accompanies her parents, Roger and Penny (George Barbier and Hedda Hopper), and Nevin Potter (George Meeker), her fiance, on an expedition to Africa to capture wild animals to sell to a zoo. Ben Alleu Bey (C. Henry Gordon) spots Eleanor and wishes her to become the one hundredth wife in his harem. When she refuses, he follows their safari.
Kom is a member of the Woonkos, a tribe of monkeys who live in a canopy and they live in obsessive fear of falling into a nearby pit, which is inhabited by other monkeys they believe to be demons. Kom refuses to believe these superstitions and claims bravery and is rude to the elder of the Woonkos. However, on the way home, he accidentally falls from the trees into the land below. When there, he meets the Lankoo tribe and finds they are in fact very similar to his own tribe. He befriends Gina, a young maid and Master Martin, the librarian and they help teach him to behave like a Lankoo. The Lankoo king is impressed by his actions, although Gina doesn't like it when he tries too hard for popularity, and briefly forgets her. However, there is also evil afoot. The chancellor Sebastian, the governess and their dim-witted side-kick, Gerard the Gormless, are up to evil plans: they will find a way for the King to die and they are poisoning his already sick daughter, Princess Ida. The King, along with most of his army, die drowning while attempting to reach the "promised land" on the other side of the poisonous lake when it was frozen. Sebastian believes his plan has worked, but the governess (who was giving the princess the poison) is given it herself by Gina and the one remaining soldier, however it is believed she is tough enough not to die, but will remain a "sleeping ugly". The film ends with Sebastian and Gerard in cages, Princess Ida as the new queen and Kom and Gina returning to the land of the Woonkos, while it is clear that the two tribes will unite. It features the song "We Are One" by Westlife.
A party from Hong Kong headed up by Johnny (Danny Lee) are exploring the Indian side of the Himalayan mountains and discover the eponymous Peking Man, a gigantic ape-like creature, along with a beautiful blond wild woman named Samantha (Evelyne Kraft) whose parents had been killed in a plane crash. Samantha was raised by Utam (the Peking Man) with nothing to wear but an animal-skin bikini. Like Tarzan, she has learned both to swing through the trees on vines and to communicate with and command the jungle animals, with the exception of a venomous snake who bites her on the inner thigh requiring the hero Johnny to suck out the poison while Samantha's leopard friend fights the snake. Shortly thereafter, they fall in love.