Koba steals guns from the human camp and shoots Caesar, but tells the apes that the humans did it in order to rally them behind him to imprison the remaining humans in San Francisco.
Caesar is not dead, and is nursed back to health by Ellie and Malcolm. His son Blue Eyes tells him everything that has occurred and apologizes for following Koba and not his father. Caesar admits that the apes have more in common with the humans than they think.
Caesar releases his loyal apes from Koba's prison bus, and confronts Koba at the top of a tower. The two fight as Malcolm confronts Dreyfus at the bottom of the tower. Dreyfus blows the tower using several blocks of C-4 after telling Malcolm that they were able to establish communication with a military base not far from San Francisco.
Up top, Caesar gains the upper hand and tells Koba he is no ape before dropping him down the tower.
Malcolm tells Caesar that the military is coming and that the apes will have to find a new home. All apes bow to Caesar, who must now lead them in a war.