Story Mode is a special mode in Super Monkey Ball 2 and Super Monkey Ball Deluxe. It is a version of the Main Game with a story to it. Super Monkey Ball: Banana Blitz did something similar with the first eight worlds.
The basic fundamentals of this mode are the same as Challenge Mode. You must roll the monkeys to the goal without letting them fall off or run out of time. However, many aspects are quite different:
- When you begin a world, you can pick any one stage from a set of ten (or twenty in Super Monkey Ball Deluxe). Unlike in Challenge Mode, there is no set order.
- You may not play a certain stage again after you have beaten it in the same save file.
- You have an infinite amount of lives. If the monkey falls out or if the timer reaches 0, you are asked if you want to retry it, which you may do as much as you like.
- Collecting bananas does nothing more than add points, and you lose the ones you have collected on a stage if you fall off or if the timer reaches 0.
- Only one player is allowed.
- You select from one of three save files to start, and you can save your progress after exiting a stage.
- Completing ten stages triggers a cutscene and changes the world.
- Only AiAi can be played.
- Your play time and total score are saved with your progress and viewable on the save file selection screen.
Dr. Bad-Boon comes from the future to kidnap MeeMee and make her his wife. Baby followed him back into the past to thwart him. After foiling his many plots, including shrinking the monkeys and building an army of AiAi robots to discredit him, Bad-Boon opts to activate his space colony to take the taste out of all the bananas in the world. After being defeated by the monkeys once again, he surrenders to the group, and the day is saved.