"The Rabbit Who Couldn't Jump and the Island of Gods" is a boy-meets-girl story about a "big mystery on a tiny island." Reon, a middle school boy who moves to Tsukito Island, where his late mother was born, reunites with his childhood friend Wako, the daughter of the Shuto family, the island's richest family. Wako is a shrine maiden of the Shuto family who oversees the island's religious ceremonies, and has supernatural powers, allowing Reon to be amazed at her ability to fly through the sky. Reon hopes to take Wako, who grew up in the countryside and dreams of the city, to Tokyo one day, but Wako laments that as a shrine maiden, she cannot leave the island. The story begins when Reon, puzzled by her words, learns of a secret about the island and the shrine maiden.