The protagonist, Masaru, has just inherited a big fortune after the death of his father. However, people are trying to get their hands on it by any means necessary, even if it means killing him. Narumi helps Masaru from being kidnapped after fighting strange figures. He finds out that they're not humans, but wooden puppets with amazing strength. After a hard fight, Narumi is forced to admit that he's no opponent for them; and just when he starts to think that Masaru will be captured, Shirogane, Masaru's watcher arrives from France with a weapon, the puppet Arlequin. Here begins the story of Karakuri Circus.
Hazumu was a shy boy who enjoyed gardening, collecting herbs, and long walks in the mountains. One day he finally worked up the courage to confess his love to Yasuna, but she rejected him. Depressed, he wandered up Mt. Kashimayama, the place where they first met, to reconsider his feelings. After getting lost, he wished upon a shooting star and received a bizarre twist of fate. Now he is a she, and she stumbles headfirst back into social life and relationships only to find that the entire landscape has changed!
Kakeru, a former elite runner at high school, is chased for stealing food. He is saved by a Kansei University student Haiji, who is also a runner. Haiji persuades Kakeru to live in the old apartment "Chikuseisou" where he plans to team up with fellow residents to enter Hakone Ekiden Marathon, one of the most prominent university races in Japan. Kakeru soon finds out that all of the residents except for Haiji and himself are complete novices.
The story takes place at Grigio Academy Boarding School where students come from two rivaling countries known as the "Black Dogs" and "White Cats." Persia and Inuzaka are leaders of their respective dorms, but they are secretly in love with each other. Now, they must keep their relationship a secret from other dorm mates while trying to avoid trouble.