The team is on vacation, sailing aboard Dr. Quest's yacht, the Sea Quest. But the vacation is cut short when a galley fire erupts, forcing everyone to abandon ship. In the chaos, Dr. Quest and Race lose track of the boys. But help is at hand as a passing ship rescues them.
The boys have drifted ashore--but where? They cobble together a scarecrow from refuse and a life jacket, then set off to find food. They're quickly surrounded by large apes and taken to a high branch in a tall tree. Several escape attempts are thwarted, and each time the boys are returned to the tree.
Meanwhile, Silky and Chopper, are listening to their shortwave radio. Former gunrunners, now ivory poachers, these two bad eggs hatch a plan to kidnap the boys. The apes first foil this, but are scared off by gunfire.
At sea, Race and Dr. Quest discover the boys' scarecrow. The friendly captain puts them ashore with supplies and a promise to send help. Shortly after they arrive, they hear the gunfire. They head towards it, but Silky gets the drop on them and relieves them of their guns. He plans to visit the airport, collect the ransom, then release the boys. But the apes have other plans.
While Chopper sleeps, an ape steals his gun--then the threat forces him to free the boys. They leave Chopper in the care of some apes, heading to the camp to free Dr. Quest and Race (with help from other apes). Silky gets the same treatment Chopper got--an ape jumps up and down on him.
The promised help arrives, and the team leaves the island, waving farewell to the apes.