The Wonderful Precure! anime is set in Animal Town, a town where animals and people live together in harmony. Second-year junior high school student Iroha Inukai is best friends with her dog named Komugi. Out for a walk one day, Iroha and Komugi encounter a mysterious creature named Gargal, who goes on a rampage in the city. Komugi suddenly transforms into a Pretty Cure named Cure Wonderful, to protect Iroha.

A teenager who was resurrected from the cemetery of the gods and demons, in the new continent formed by the collision of the East and the West ten thousand years later, searches for the truth of the fall of the gods and demons ten thousand years ago, as well as the pursuit of his lover Yuxin, the whereabouts of his parents and the reason for his resurrection. The protagonist develops, and finally leads to a story about the six paths and the chess game of heaven and earth.

The anime follows the daily life of PuniRunes—mysterious creatures who love to be coddled—and Yuka, a fourth-grade girl who loves soft, squishy things.