Three of the apes from the second movie, "Beneath The Planet of The Apes", Cornelius (Roddy McDowell), Zira (Kim Hunter) and one other ape, Dr. Milo, escape from the future in Charleton Heston's space ship and arrive on earth in the past (our present), just as it was being blown up by Charleton Heston in the second movie. They at first are treated like normal apes, until Zira is given a banana and refuses to eat it, by saying "I loathe bananas." The two scientists, a male and female, are at first shocked by their speaking, but learn to accept them.
Shortly after, the third ape is accidentally killed by one of the present day apes in the next cage beside them. They soon are brought before some kind of hearing, where they are eventually unchained and let go to live amongst us in a hotel. They are given a shopping spree, and eventually Zira announces that she is pregnant. Later on, Zira is given some kind of truth serum, and is questioned on what had happened in the future to the world and what they use to do to humans, because they feel that they are not being totally truthful about what happened in the future.
When the government finds out the truth, they decide that these two apes should be exterminated, to prevent what happened in the future, to ever happen again. But, the two scientists that they befriended, helps them to escape to a nearby traveling circus, run by Ricardo Montalbon. He helps the two, by letting Zira give birth to her ape child there. She then exchanges her baby for another modern day ape's baby, there at the circus. They then take the other apes baby and leave the carnival. They end up going to an abandoned ship, where the government bad guys catch up with them.