Nate, Whisper, and Jibanyan travel to the past to help Nathaniel and Hovernyan create the Yo-kai Watch when dark forces conspire to undo the history of the watch.

When the evil Yo-Kai Kin, Gin, and Do steal the Yo-Kai Watch from Keita one night so they can help their master Tokio Ubaune prevent humans and Yo-Kai from being friends, Keita finds help in the Yo-Kai Fuyunyan, who takes Keita, Whisper, and Jibanyan back in time 60 years to when the Yo-Kai Watch was first invented by Keita's own grandfather Keizo while he was a boy. Together, the two boys fight Tokio Ubaune and her evil Kaima Yo-Kai minions to save the world from her evil plans.

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