The story of Puzzle Bobble Everybubble! brings Bub, Bob, Peb, and Pab to Rainbow Island, where Miniroon, a mysterious character similar to Bub lives. One day, Miniroon suddenly starts to emit a large number of bubbles, covering the whole island and causing problems for its residents. Time for our four friendly bubble dragons to step in and help Miniroon, whose bubble-blowing is bad news for the island!

To clear each stage, players need to remove bubbles by connecting three or more of the same color - either on their own or with the help of fun and entertaining items and gimmicks.