The game boasts nine courses, three times of that from the original Puyo Puyo Fever. Each of the three main characters (Amitie, Raffina, and Sig) has three courses, each with a different story. In general, the main plot of the WakuWaku course involves meeting Lemres, a wizard from the neighboring town who is visiting Primp Magic School, and the plot of the HaraHara course involves stopping Klug, who has become possessed by his book. Each character sets off to do these things in their own way, and usually those things not being their initial intentions.