In Nazo Puyo mode, Arle Nadja is working through Magic Junior High's puzzle curriculum on her way to graduation. Players choose one of three difficulty levels—First Year, Second Year, or Third Year—each containing a unique set of opponent characters. Arle must clear ten puzzles against each character to advance. First Year opponents include Skeleton-T, Draco Centauros, and Sasoriman; the Second Year brings Harpy, Zombie, and Rulue; the Third Year culminates in battles against Zoh Daimaoh, Minotauros, Schezo Wegey, and Satan.