The Simian Senate is holding a lop secret session to debate the rumors of intelligent humans begun after one of Urko's soldiers returns delirious from the Forbidden Zone. He claims to have seen a flying craft fall out of the sky, crash in the dead lagoon and three humans (Bill, Jeff and Judy) emerge and raft to the shores. Gen. Urko demands that all the humans be destroyed, but after hearing all sides, the Lawgiver (Zaius) closes the debate by announcing that the Supreme Council will decide the fate of the humanoids. Later, at a press conference, Zaius and Urko announce their plans to lead an expedition into the Forbidden Zone to verify the soldier's story of a spaceship in the lagoon. Zira and Cornelius decide to warn Bill and Jeff of the expedition. Using a mirror, Cornelius signals the men for a meeting. He explains that if the ship is found, Urko will have all the evidence he needs to begin his annihilation of the humans. The apes believe that Bill and Jeff have infected the humanoids with the ability to think and, as ape law states, they cannot be allowed to gain intelligence. Bill and Jeff decide to beat Urko to the ship, salvage the laser and blow up the spacecraft. Bill asks Nova to lead them to the lagoon. Frightened, she agrees. The next day, Zira and Cornelius watch as the expedition leaves town, worrying for Bill, Jeff, and Nova's safety.
As the expedition travels farther into the Forbidden Zone, flames and lightning and other strange images block their way. Urko decides to make camp for the night and proceed in the morning. Suddenly, a flaming skull appears in the sky. The frightened soldiers want to turn back for the City, but Dr. Zaius, skeptical of what they have been seeing, exposes the images as mere illusions. By morning, Bill, Jeff and Nova have reached the lagoon ahead of the army. Luckily, the Venture is still partly above water. They raft to the capsule and Bill swims down to get an oxygen mask out of the ship. The army is advancing rapidly, but they are stopped once again by the mysterious flames. Urko is enraged and orders his driver to proceed. Diving once again, Bill retrieves the laser and they return to shore to test it. Confident the laser is functioning well, Bill swims back to the ship and sets the self-destruct mechanism to detonate in five minutes. But on his way out, a giant sea serpent blocks his way. He swims into a cave to hide. Jeff arrives and drives the monster off with a laser blast just in time for them to reach the shore before the ship explodes. The army arrives and sees the serpent bobbing around on the surface. Zaius deduces that what the delirious soldier saw was the serpent, not a space craft. They return to Ape city where Zaius announces in a press conference that the rumors of intelligent humans are false. Soon, the newspaper headlines read: "Planet of the Apes Safe!"