18 year old Jason and his best friend Tann journey to the mysterious Kong Island hidden in the heart of the Bermuda Triangle. With them is their college Professor, Dr. De La Porta. After a close encounter with dinosaurs, Jason is reunited with his grandmother, Dr. Jenkins, and Kong. With them is the beautiful Jungle Girl, Lua. Dr. Jenkins has resurrected Kong via DNA splicing and the Cyber-Link, a communication and data link to the Web. With the Cyber-link a person can also ""merge"" with other animals. De la Porta threatens Dr. Jenkins in an attempt to steal her research and discover the location of the magical Primal Stones. He uses the Cyber-Link to merge with a sabertooth tiger becoming the monstrous Badkat. Jason merges with Kong and drives De La Porta away after an epic battle.

On Kong Island, the evil Professor Ramone De La Porta forces Dr. Jenkins to take him to the location of the powerful, mystic Primal Stones. Jason, Tann, and Lua frantically search the exotic Island for the kidnapped scientist. They find Dr. Jenkins and De La Porta in the ruins of an ancient temple. De la Porta merges with a giant prehistoric bear, becoming Slothbear, and attacks them. Jason merges with Kong and defeats him

De La Porta takes the Primal Stones from an ancient temple on Kong Island, which upsets the Island's mystic and environmental balance. Earthquakes, storms, and volcanoes shake the Island. They find the Professor, but De La Porta merges with a giant prehistoric cave snake. Kong goes head to the head with the newly created monster, but is buried in a cave-in. Drawing on his memories, he finds the strength to slowly free himself. De La Porta attempts to leave the Island in a seaplane, but Jason, Tann, and Lua battle him until Kong arrives to help. De La Porta eventually escapes with 6 of the 12 Primal Stones. Jason vows to hunt him down and retrieve the Stones.

The theft of the Primal Stones from Kong Island threatens to awaken the ancient demon Chiros. Lua journeys alone to Chiros' ruined temple in an attempt to imprison him. She is captured and brainwashed by Harpy, one of Chiros' servants. They journey to the Island's volcano and set the demon free. Jason, Kong, and Tann arrive and Chiros awakens the monster Ominous to stop them. Jason merges with Kong and confronts him. In the fight Kong's anger transforms him into the gigantic Mega-Kong. He easily defeats Ominous forcing Chiros to retreat.

Jason, Tann, Lua, and Kong travel to New York City in an attempt to stop a series of robberies of ancient tablets connected to the Primal Stones. They discover that De La Porta is behind the thefts and is trying to learn how to unlock the power of the Stones. Kong and Jason are forced to battle two monstrous Cyber-Link creatures, BadKat and Slothbear, in order to stop De La Porta.