The story takes place after the events of the fourth film and focuses on 11-year-old Keisuke Amano, who is Natsume's younger brother. Despite not believing in supernatural phenomena, he becomes suspicious when his sister returns home late frequently. Upon investigating, he discovers that she has been performing her duties as an exorcist alongside her friends Touma and Akinori, running a Yo-Kai detective agency. As a result, Natsume decides to allow him to join in on their activities, including investigating Youkai crimes and battling evil Youkai to maintain peace throughout the city.