Ape City is flooded from when the moon exploded. Cornelius saves chimp Lucius' life while Zaius' daughter gives birth with the help of gorilla Marcus. Then Zaius finally confronts Brother Corvin, a scholar who knows a little bit too much information about mankind's history, such as the location of The Bunker. It's an old missile control center. Zaius suspects that Corvin is an impostor since he's violated the "Ape shall not kill Ape" rule. He's not wrong. Zaius puts the suspect under guard but then the two gorilla guards shoot are mind controlled and shoot each other. Corvin escapes. Zaius finds and shoots him, saying "Ape does not kill ape. Therefore you are not an ape" . At this, the impostor pulls off his ape mask to reveal the hideous mutant human underneath. He says that he wants the end of the world and hints that ape society has been infiltrated by impostors, which freaks out Zaius, who has his soldiers burn the mutant's body.
However, Zaius doesn't know that his daughter is dead from childbirth and his wife injured. The story ends with Zaius holding his new grandbaby and then there's a shot of the Forbidden Zone, where the mutant humans are praying to the Alpha-Omega bomb...
Again, this adds a great backstory to the events of the original film series. Highly recommended.