The story shows the Super Monkey Ball team and all the Jungle Island inhabitants happily enjoying their day, when suddenly, Dr. Bad-Boon's airship flies over the land and vacuums up all of the bananas. AiAi demands he give back all the bananas, but he will only do so if MeeMee marries him. MeeMee refuses, so Bad-Boon flies off, and the Super Monkey Ball team jumps into action. Dr. Bad-Boon's first nefarious scheme is to blow up Jungle Island by making a volcano explode with a time bomb. He leaves it floating inside of it, and the team finds it. GonGon says he will destroy the bomb, despite MeeMee's pleas against it. He punches it out of the volcano, and it lands all the way in Bad-Boon's airship. It sinks into the sea, which drive Bad-Boon to swim away with the team chasing after him.