Ms. Accord, a teacher at the Primp Magic School, has lost her Flying Cane, the equivalent of a magic wand, and claims to have a reward for the student who can find it. The player plays the role of either Amitie or Raffine, students at the school, as they venture across the Puyo Pop Fever world to find the cane, while meeting many wacky characters along the way and battling them. Raffine's course contains more difficult gameplay and alters the characters the player meets, as well as which character actually finds the wand. When playing as Raffine near to the end of the game, it is revealed that Accord never actually lost her flying cane. Raffine then plans on revealing her and Popoi's secret, but fails in her ending, as she is knocked unconscious by Ms. Accord, losing all memories of the flying cane incident. She regains consciousness near her school where Amitie and her friends congratulate her.