Keisuke Amano, Natsume's brother who doesn't believe in supernatural phenomena. But as he notices his sister is frequently comes back home late, he decided to stalk her, only to find out she is exorcising evil Yo-kai and running a Yo-kai detective agency. With their secret revealed to him, Natsume decided to let him tag along in her activities as they investigate Yo-kai crimes and take on evil Yo-kai to maintain peace all over the city.

Shuichi Kagaya is an ordinary high school kid in a boring little town. But when a beautiful classmate is caught in a warehouse fire, he discovers a mysterious power: he can transform into a furry dog with an oversized revolver and a zipper down his back. He saves the girl’s life, sharing his secret with her. But she’s searching for the sister who killed her family, and she doesn’t care how degrading it gets: she will use Shuichi to accomplish her mission…

新エネルギー資源の発見によって造られたメガフロート都市・ベイロンシティ。 そこで小さな会社を営む青年・シュウ。 彼は日頃の金遣いの荒さからひもじい生活を送っていた。 そんなシュウを心配し、彼の事務所兼自宅に通う一人の少女・キサラ。 彼女はベイロンシティ内の高校に通いながら、仕事の事務作業から家事まで面倒を見る。 そしてもう一人、シュウが以前に所属していた会社の先輩であり、 元恋人でもあるアヤノも彼のことを気にかけていた。 太平洋に浮かぶ人工島で巻き起こる