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.

Mu-tan and his pirates board Dr. Hayden's boat and take him and Leslie captive. Upon surfacing, Link goes to their rescue, only to be thrown overboard. After taking the treasure, Mu-tan blows up their boat.

Link is attacked by a shark while swimming to the nearest beach, but manages to frighten him away. He reaches the beach, where a leopard finds him and a fight ensues; luckily, he is not harmed. The leopard retreats and Link collapses on the sand.

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.

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.

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.

Upon reaching the shore of the island where Dr. Hayden had told them they would find the lost city of Tobanya, Mu-tan threatens Dr. Hayden with his life if the lost city is not found. Mu-tan does not believe the doctor is telling the truth and he and Chu fight over who is captain.

Upon returning to their cave, Morgan, Chongo and Link are attacked by some natives who were waiting for them to return. After a good fight, they rid themselves of the natives. Meanwhile, back at the shore, Mu-tan has tied Dr. Hayden and Leslie so they cannot escape.

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.

Dr. Hayden and his daughter, Leslie, begin their journey to the cave with Morgan, Chongo and Link. After a dangerous trip, they return to the cave.

In the cave, Dr. Hayden finds his brother's map, which shows where the lost city of Tobanya is located. Suddenly, the earth begins to shake...an earthquake. They all run out of the cave, but Dr. Hayden decides to go back for the map.

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.

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.

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.

Morgan, Chongo, Link, Leslie and Dr. Hayden make their way to a deserted village. They think they will be able to take refuge there for a while, but Mu-tan had reached the village before them. Upon their arrival, he takes them captive.

Morgan, Chongo, Link, Leslie and Dr. Hayden are all Mu-tan's captives once again. Dr. Hayden reassures his group that Mu-tan needs him to read the map to the lost city.

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.

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.

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.

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.

Morgan, Chongo and Link fight the Skeleton Men and manage to escape into the jungle. Leslie is brought to the hideaway cave of the White Savages and is held captive while Dr. Hayden continues looking for her. Morgan, Chongo and Link find Dr. Hayden and join him in searching for Leslie.

Morgan, Chongo, Link and Dr. Hayden continue searching for Leslie. They stop to rest a moment and are spotted by the White Savage guards. They manage to escape and discover the entrance to the cave, arriving just in time to save her from a boiling pool.

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.

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.

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.

Dr. Hayden, Leslie, Link, Morgan and Chongo are attacked by a swarm of bats, but manage to escape. They reach the end of the cave and then travel through the jungle. They finally arrive at the lost city of Tobanya, only to find Mu-tan and the Skeleton Men, who take them captive

Mu-tan plans to throw his captives into the lions' den. The Chief of the Skeleton Men intervenes and orders one of them to fight Mu-tan. Link is chosen, and if he wins, their lives will be spared. They fight a tug-of-war over the lions' den.

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 takes Dr. Hayden and his party on board his boat. A proposition is made to Dr. Hayden by Mu-tan...that he helps Mu-tan find the treasure in the lost city of Tobanya, and Leslie will be held ""under protective custody"" until their return.

They all return to the island to retrieve the treasures of the Lost City. They are spotted by the Skeleton Men. Chongo creates obstacles to slow down the Skeleton Men, while Morgan, Link, Dr. Hayden and Mu-tan take another path, which they find full of treacherous obstacles.

Finally, they reach the lost city again. By carefully studying the map, Dr. Hayden leads Mu-tan to the treasure. As Mu-tan counts his gold and jewels, the Skeleton Men surround them all.

Mu-tan has to turn over his gun to the Skeleton Men. While their attention is drawn to the others, Chongo disguises himself as a Skeleton Man and succeeds in knocking a few of them out. Morgan takes a cue from Chongo and a fight begins.

Dr. Hayden, Morgan, Link and Chongo are fortunate enough to escape the cave, leaving Mu-tan and his men behind as prisoners of the Skeleton Men. They head for their boat, only to be trapped once more by the Skeletal Natives.

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.

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.