During an interview with Jungle Island (a fan website dedicated to the Super Monkey Ball series), concept artist Keith Webb revealed that the character Future AiAi came about after he came up with an idea for a space monkey that would appear at certain points in the game to give players power-ups (later spells), and was intended to be an homage to the Bomberman series by Hudson Soft. He was originally supposed to wear a white spacesuit, but before Webb could finish coloring in the artwork, the character modeler making the character in 3D chose a red color that ultimately stuck. Webb had later joked about the character being AiAi from the future (the reason why he had the power-ups was because he had gotten them from himself), and the idea stuck as well.

Beating the game with 100% completion unlocks a final cutscene which reveals that the monkey who gave you chants throughout the game is Spoiler:AiAi from the future. This cutscene further reveals that Spoiler:AiAi and GonGon invent the magic energy balls that the series' cast run around in, Baby is AiAi's future son, and that MeeMee is Baby's mother.

Various posters are hung throughout Monkitropolis that feature monkey-themed parodies of other Sega games. These include Virtua Cop 2, Football Manager 2006, and Virtua Tennis World Tour.

In an attempt to make the game more accessible and add more depth to the series, Sega opted to focus more on the game's plot compared to previous titles, which primarily focused on the gameplay, to try and take the series' characters "into the next sort of iconic level".