The full plot of Beneath the Planet of the Apes moves from an ape invasion plan to a buried city of mutants and ends with the destruction of the planet.
In Ape City, General Ursus rallies the apes to invade the Forbidden Zone, over the objections of Dr. Zaius. Brent is wounded and treated by the chimpanzees Cornelius and Zira, who tell him about Taylor. Brent and Nova are then captured, but Zira helps them escape into a cave. The cave turns out to be a ruined subway station, and Brent realizes he is standing on a devastated future Earth.
In the ruins below the city he finds telepathic mutant humans who worship an old atomic bomb. They use illusions and mind control on him, and he discovers Taylor held captive. Their leader Mendez forces the two men to fight until Nova's scream breaks his hold, and together they kill him. Taylor explains that the bomb is a doomsday weapon.
The apes then invade the underground city and a battle breaks out. Nova is killed, Mendez raises the bomb into position and is shot, and Taylor is wounded while confronting Zaius. Brent kills Ursus and is shot dead himself. A dying Taylor presses the detonator and the whole planet is destroyed.
So, what happened to the humans in Beneath the Planet of the Apes? Nova dies in the fighting, Mendez is shot, and both astronauts, Brent and Taylor, die as well. Taylor's last act sets off the bomb, and the planet is destroyed.