Set after the events of the fourth film, the series focuses on 11-year-old Keisuke Amano, Natsume's younger brother (both are children of Keita Amano and Fumika Kodama from the original Youkai Watch anime), who does not believe in any supernatural phenomena around him. However, noticing that his sister frequently comes home late, he decides to follow her, only to discover that she is performing her duties exorcising evil Youkai alongside her friends Touma and Akinori, and running a Yo-Kai detective agency. With their secret revealed to him, Natsume decides to let him join her activities as they investigate Youkai crimes and take on evil Youkai to maintain peace throughout the city.