Puyo Pop for the Game Boy Advance was the first game in the series to be developed by Sonic Team. It combines Puyo Puyo 2's mechanics with an all-new story mode.

The Dark Prince is once again up to no good. He splits up five gold runes, and they are handed off to different individuals across the globe. Dark Prince then sets up a Puyo Puyo contest. Carbuncle runs off for it, and Arle give chase, thus starting her strange journey to collect the runes and find Carbuncle. At the end, it is revealed that the Runes are actually a ticket for Dark Prince and Arle to go and bathe at some Hot Springs. Arle, however, doesn't realize that the ticket is for her and throws it away, foiling Dark Prince once again and leaving him to cry hysterically.