The beginning of the movie looks like the same shot of the ocean and cliffs from the end of first Apes movie, when Taylor sees the half buried Statue of Liberty. Yet when we hear a helicopter and see the human pilot we know something is awry, never mind the fact that the entire earth was destroyed at the end of BENEATH THE PLANET OF THE APES. The army brings a battered looking spacecraft to shore, helps out the three astronauts--and are shocked when they take off their helmets to reveal they are chimpanzees. They are Cornelius (Roddy McDowell), Zira (Kim Hunter) and Dr. Milo.
At first, when the apes are taken to the Los Angeles zoo, they keep quiet. It's when Zira gets irritated being tested by Doctors Lewis Dixon (Bradford Dillman) and Stephanie Branton (Natalie Trundy, who also portrayed one of the mutants in BENEATH THE PLANET OF THE APES) that she talks. The government questions them but they keep quiet about coming from a future world where humans are basically animals. The President of the U.S. is fairly laid back in regard to the intelligent apes but his science advisor, Dr. Otto Hasslein (Eric Braeden) views them as a threat from the get-go. The public accepts the talking primates and they become overnight celebrities and are shown the city. And Zira faints when she's in the natural history museum. They think she passed out from seeing a stuffed gorilla but she says it's because she's pregnant.
Eventually, they let the truth slip and Cornelius and Zira are taken to a military base and interrogated. Cornelius explains he has access to secret documents the Orangutans had, that tell of how apes were kept as pets for two hundred years by humans after all dogs and cats became extinct, then how they revolted 300 years later when they were slaves. But the intelligent apes traveling back in time changes all this, speeding everything up by 500 years because their son, Caesar, will begin the ape revolt twenty years later in CONQUEST OF THE PLANET OF THE APES. The U.S. government then decides to have Zira's child aborted and the adults steralized. Before this happens they manage to escape, though Cornelius accidently kills an orderly who is bringing them a tray of food. They're helped by the two human doctors, who arrange for them to hide out in the Circus of a friend of theirs, Armando (Ricardo Montalban). He loves the apes and introduces them to a chimp he has that recently gave birth. However, soon after Zira gives birth they have to flee the circus and so take refuge in an abandoned freighter in the bay. Otto Hasslein, intent on preserving mankind's future, tracks them down and ends up killing Zira and her infant son. Cornelius is shot by the military and falls to his death. It's one of the most depressing ends of a movie, ever. It does end on an up note, as the final scene is at Armando's Circus--and we see the infant chimpanzee say "Momma, momma." Zira had swapped her kid with that of the other chimp.
It's a story that's continued in CONQUEST OF THE PLANET OF THE APES...