Kong: King of Atlantis is based closely on the companion movie to Kong: The Animated Series, incorporating the plot of the video version in an action-packed, side-scrolling adventure.

When an ancient prophecy starts to come true, the sunken city of Atlantis begins to rise. The evil Queen Reptilla plans to trick Kong into becoming her King, using him as her slave to unite the warring clans of Atlantis for her own evil gains. In a race against time, Jason must convince Kong that Queen Reptilla is evil, in the hope that together they can save the islands of Kong and Atlantis and their inhabitants.