The objective of Super Monkey Ball 2 is to guide a monkey trapped inside a plastic ball through a maze to the goal. There are three variations, story mode, challenge mode, and practice mode. In story mode you have an unlimited number of tries to complete a stage, and after clearing 10 stages a movie clip is shown followed by a new world of 10 stages. In challenge mode, you have a limited number of monkeys and a time limit to complete numerous levels of increasing difficulty. In practice mode, you can play any stage already completed in the other two modes.

In addition to the main game options, numerous party games are also included. These are monkey race, monkey fight, monkey target, monkey billiards, monkey bowling, monkey golf, monkey boat, monkey shot, monkey dogfight, monkey soccer, monkey baseball, and monkey tennis. The party games can be played by one to four players.

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.