Bub and Bob are once again transformed into bubble dragons and have to climb up the Rainbow Tower to fight the Super Dark Great Dragon, while collecting potions to turn back into human form.

Bubble Memories does very little to change the gameplay of the series, except for introducing giant enemies on some levels, different bosses, and a way to blow giant bubbles after charging up (especially for killing the giant enemies). (Giant bubbles can be blown by charging up the character. The bubble button is held until the character's horns begin flashing, and then releasing the button.) There are a total of 80 levels, while the last 10 levels can only be accessed by collecting 7 potions.