Keita, Whisper, Jibanyan, Inaho, Usapyon, and all of their Yo-kai friends embark on five unique adventures that all end up tied together in the end.
When the evil Yo-Kai Kin, Gin and Bronzlow makes the Yo-Kai Watch disappear from time so they can help Dame Dedtime prevent humans and Yo-Kai from being friends, Nate Adams finds help in the Yo-Kai Hovernyan, who takes Nate, Whisper and Jibanyan 60 years to the past, when the Yo-Kai Watch was first invented by Nate's grandfather, Nathaniel Adams, while he was a boy. Together, the 2 boys fight Dame Dedtime and her evil Wicked Yo-Kai minions to save the world from her evil plans.
A giant whale appears and flies above Sakura New Town. With the whale’s sound of crying, some changes occur to Kenta Amano and Yokai.