The staple gameplay mode, Great Transformation, allows characters to take on child or adult forms, giving smaller or bigger Puyo respectively.
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The game opens with a storm of Puyo falling down onto Earth, flooding a high school in its wake. Ringo Ando, a student who witnesses the flood, trembles until Arle Nadja appears. She teaches Ringo how to play Puyo Puyo and fight the many enemies with her skill. Arle soon finds herself being endangered and runs off, and Ringo sets out to find her, encountering old and new friends and rivals, using a special ability: she is able to transform into an adult or a child while playing the game, affecting the Puyo size in the process.
After a match with Klug, Ringo decides that in order to solve the problem, she must travel to seven power spots of the planet, encountering the strongest opponents. During the trek, she discovered that Arle has become possessed by a new adversary, Ecolo. When Ringo comes upon the newly transformed Dark Arle, she defeats her, reverting her to normal. Ecolo decides to bury the universe in Puyos just for amusement. Ringo, Arle, and Amitie team up with her to save the day. Ecolo is defeated, and everyone returns home.