One day, while searching for bugs in the woods, a boy named Nate (Keita in Japan) comes across a peculiar capsule machine next to a sacred tree. When he opens one of the capsules up, it brings forth the Yo-Kai Whisper, who gives Nate a special device known as the Yo-Kai Watch. Using this, Nate is able to identify and see various different Yo-Kai that are haunting people and causing mischief. Joined by the cat Yo-Kai Jibanyan, Nate and Whisper start befriending all sorts of Yo-Kai, which Nate can summon to battle against more ill-intentioned Yo-Kai that happen to live in his town, causing terrible trouble. He also goes on adventures around the town with his Yo-Kai partners to help his human friends Bear (Kuma), Eddie (Kanchi), and Katie (Fumi-chan; also the choice for the female player character in the video games) deal with their various problems, often caused by other Yo-Kai. Later, a new girl named Inaho moves into town, in a different homeroom class from Nate, and receives her own Yo-Kai Watch, meeting the Yo-Kai Usapyon, who wants her help in restoring the happiness of a scientist he accidentally upset, before they open up a detective agency to investigate many Yo-Kai "crimes" plaguing the city.