Set a couple of years after the events of Polka Aqua 2, the storyline follows the younger cousins of the former Champions as they move into their new home in San Francisco. After visiting their father, who serves as the curator of the local Art Museum, players rescue Professor Palm from a wild Skitty once again to obtain their very first partner. From there, players set out on an adventure to solve mysteries, save the world, and train up their team inside a crossover universe filled with iconic television and movie characters.