Skull Island is one of the locations that Mickey Mouse can complete quests in. This section of the Pirates of the Wasteland, is modeled after Park rides like Pirates of the Caribbean and films like Peter Pan. It is based on the same island of the same name from Peter Pan.
In one mission, Mickey travels to Skull Island to deal with a machine that's turning Animatronic Captain Hook's pirate crew into robots. The player has three choices: filling the tanks with Thinner which destroys the machine, but won't turn the robotic victims back to normal. Filling them with Paint would reverse the process. Turn them back into pirates, and a chest for you to fill in with paint at the machine awaits. This will also unlock a movie clip in the Extra menu, or, the player may ignore or jam the machine entirely, opening up even more choices and quests upon Mickey's return to Ventureland.
The player must also find and erase 3 anchors, which are hidden in cave islands near the Skull Island, in order to free Smee's ship. This allows Mickey to ride to the Jolly Roger and face Captain Hook.
Skull Island is played out like layers. With ships and enemies at the very edge, and tunnels and caves at the very center as it spirals upwards at the very middle, which gives the player a view of the entire level.