As they approach Mu-tan's boat, they are spotted by Leslie's captor, and he begins shooting at them. Chongo and Link swim to the boat and rescue Leslie. Dr. Hayden and Morgan join them. They then make their way back. Morgan tells the others that he and Chongo have decided to stay on the island, since it has become the life they know best. Dr. Hayden, Leslie, and Link reluctantly bid their good friends goodbye, and they head back to civilization.
Chongo had managed to climb high on the rocks while the Skeleton Men surrounded the others, and threw a net over the group closest to his friends. In order to frighten off the others, Morgan throws a grenade. They then make their way to the ocean, where they climb on board a rubber raft left there by Mu-tan.
In the life or death tug-of-war between Link and Mu-tan, Link manages to overpower Mu-tan, but spares his life. Dr. Hayden and his party are freed by the Skeleton Men, but are told to leave the island, never to return under threat of death. While they are put into a boat by the Skeleton Men, Mu-tan, having escaped, joins his men on his boat. Spotting Dr. Hayden and the others on the river, Mu-tan capsizes their boat.
Mu-tan returns to the Skeleton Chief to demand more men. The Chief grants his request, but orders Mu-tan to capture Dr. Hayden and his party or die. As Dr. Hayden and the others travel through the caves to the lost city of Tobanya, Chongo is attacked by a giant bat, which Morgan is able to scare off. However, upon entering another cave, they are not so lucky.
A fight begins between Mu-tan and his Skeleton Men and Dr. Hayden, Morgan, Link and Chongo. Mu-tan escapes, but drops the map in the river. After defeating the Skeleton Men, Dr. Hayden and his party follow Mu-tan, but the Doctor tells them to let him go, that it is more important to find the map. They begin their search and Chongo finds the map.
Since the map contains the key to the only path to the sea, they decide to retrieve it and arrive at the ravine where Mu-tan had dropped it. They spot the map on the cliffs. At the same moment, they spot Mu-tan on the other side of the river with the Skeleton Men. He has joined forces with them and has also come to retrieve the map.
Dr. Hayden returns to discover Leslie is gone. He immediately goes into the jungle to search for her. Meanwhile, Morgan and Link are being chased by the Skeleton Men, first on land and then on the river. Chongo catches up in time to aid in capsizing the Skeleton Men's boats. They come ashore, only to be surrounded again by more Skeleton Men.
Continuing through the jungle after Mu-tan, Morgan and Link catch up to him, only to see him held captive by the Skeleton Men. They are also spotted, and the chase begins. Too impatient to wait, Chongo finds a rifle for Dr. Hayden to use as protection, and then leaves them to search for Morgan and Link. While Dr. Hayden investigates some odd sounds, Leslie is carried off by some mysterious White Savages.
Morgan tries to pull Link out of the dangerous waters. Unable to help him, he jumps into the water and wrestles with the alligator, saving Link. He manages to pull Link out of the water, and they continue chasing Mu-tan. Meanwhile, Chongo and Leslie find Dr. Hayden back at the village, and they wait together for Morgan and Link to return.
While Dr. Hayden is double-talking Mu-tan in the reading of the map, the others manage to escape from their bonds. They fight off the pirates. Mu-tan, hearing the commotion, runs away with the map. Morgan and Link chase after him. They follow him over a narrow bridge, but Link falls into the alligator-infested waters.
Link is hanging dangerously at the edge of the falls. Morgan luckily reaches and saves him just in time. They continue through the jungle, all the time being watched by the Skeleton Men. Finally, they find themselves surrounded by them. They manage to scare them off and make their escape, but the Skeleton Men follow them.
Dr. Hayden, Morgan, Chongo, Link and Leslie travel down the river in their makeshift boat as far as they can, and then start through the jungle. One of the obstacles they come to is a treacherous waterfall, which they must cross. Link, the last one to go, loses his footing and slips into the swirling waters.
When the earthquake subsides, Morgan, Chongo, Link and Leslie try to rescue Dr. Hayden, who is trapped in the cave under tons of earth and rock. Chongo discovers an opening in the cave which leads to where Dr. Hayden is. They rescue him and recover the map. They then build a makeshift boat so they can find the inlet where they believe the boat is.
Chongo has discovered a ship anchored off the island. He, Morgan and Link run to the beach where they find Mu-tan and his pirates. They scare them off and rescue Dr. Hayden and Leslie. Morgan tells Dr. Hayden he had found a boat off an inland island along with some maps and other articles. Dr. Hayden feels that these articles and maps belong to his brother, Philip, who was lost near the islands some years before. They decide to go back to the cave and take a look at the map so they can start their search right away.
Surrounded by headhunters, they (Link, Morgan and Chongo) must fight the natives. They manage to escape with the natives in pursuit. After a few harrowing experiences, they outwit the natives and return to the safety of their cave. Meanwhile, Mu-tan and his men reach the shore with Dr. Hayden and Leslie as their prisoners.
Morgan and Chongo show Link the traps set all over the island by the headhunters. In their travels, they come across these traps and Link is saved by Morgan many times. Chongo sees smoke in the distance and, aware that the headhunters are close by, they start to run back to their cave, only to find themselves surrounded by the headhunters.
Morgan and Chongo find Link Simmons on the beach, where he had collapsed. At first, Link is afraid of them, but Morgan tells him that they were merchant marines who were thrown overboard and they, too, were washed ashore. They take Link to their cave and explain that the natives of the island are headhunters.
Searching for the lost city of Tobanya, Dr. Hayden, his daughter, Leslie and his assistant, Link Simmons, discover their first clue in uncharted waters of the South Pacific. Link and Leslie find a treasure chest amongst the remains of a sunken ship. They bring the treasure on board. Just then they spot a boat approaching. It is Mu-tan and his band of pirates. Dr. Hayden covers the treasure as Mu-tan's boat comes alongside their own.