In a place called Major Land, the "Melody of Happiness" is due to be played, spreading happiness throughout the world. However, an evil man named Mephisto steals the Legendary Score, plotting to turn it into the "Melody of Sorrow" to spread sadness across the land. Aphrodite, the queen of Major Land, scatters the Notes that make up the Legendary Score into the human world and sends a fairy named Hummy to Kanon Town in order to recover them.

There, Hummy meets two girls, Hibiki Hojo and Kanade Minamino, who are chosen to become the Suite Pretty Cures in order to recover the missing Notes and protect everyone's happiness.