Hyuuga Saki and Mishou Mai meet in the forest after following strange lights. Five years later they reunite under the Sky Tree, where they meet Flappy and Choppy, two spirits from the Land of Fountains; they have fled from Akudaikaan, the evil ruler of Dark Fall, who has taken over six of the seven fountains that protect the life-giving World Tree. They give Saki and Mai the power to transform into Pretty Cure, so they can fight Akudaikaan's minions and restore the fountains.

In the middle of a karaoke contest, Saki and Mai find that time has suddenly stopped. Following some spirits, they wind up in the Land of Clocks where they find Sirloin, a warrior from Dark Fall who is keeping the Infinite Clock hostage.

Naturally, Pretty Cure won't stand for this, and they begin to battle. But can they stop fighting with each other first?