When the evil Kin and Gin steal the Yo-kai Watch from Nate Adams one night to help their master Dame Dedtime prevent humans and Yo-kai from being friends, Nate finds help in the Yo-kai Hovernyan who takes Nate, Whisper, and Jibanyan back in time 60 years to when the Yo-kai Watch was first invented by Nate's own grandfather, Nathaniel while he was a kid. Together, the two boys fight Dame Dedtime and her evil Wicked Yo-kai minions to save the world from her evil plans.