When Keita frees Whisper, a ghost-like yōkai, from 190 years of imprisonment, Whisper pledges to protect Keita from supernatural dangers. Whisper also gives Keita a watch that allows Keita to see other yōkai. Together with the twin-tailed cat spirit Jibanyan, they encounter lots of yōkai-related problems and solve them.

Adapted from the video game series of the same name, NiNoKuni follows high school peers Yuu and Haru who must travel between two separate yet parallel worlds to help save their childhood friend, Kotona, whose life is in danger. In this magical quest complicated by love, the three teens will be tasked with making the ultimate choice.