As summer break comes to an end, Nishikata is stoked to try out his newest pranks and finally outdo his classmate Takagi once and for all. Despite his losing streak, he is slowly getting to know the unrelenting workings of her crafty mind. However, he soon realizes that Takagi's motivations behind her teasing may not be what he initially assumed. One thing is certain, though: each fun-filled day of strategizing and competing brings the two closer than ever.

Failed kamikaze pilot Ken Asuka becomes a rough, tough hooligan who settles all of his problems with karate, until he learns about the legendary swordsman Musashi Miyamoto in the novels of Eiji Yoshikawa. Resolving to live his life like Musashi, he begins to take karate more seriously. Based on a manga by Ikki Kajiwara and Jiro Tsunoda, itself inspired by the real life of Yasunobu Oyama, the founder of the hard-knock Kyokushin Karate school. (Source: The Anime Encyclopedia)

Having a friend that knows you inside out should be a good thing, but in Nishikata's case, the opposite is true. His classmate Takagi loves to tease him on a daily basis, and she uses her extensive knowledge of his behavior to predict exactly how he will react to her teasing, making it nearly impossible for Nishikata to ever make a successful comeback. Despite this, Nishikata vows to someday give Takagi a taste of her own medicine by making her blush out of embarrassment from his teasing.

Narumi Katou is a middle-aged man who suffers from the bizarre ZONAPHA Syndrome: a rare and inexplicable disease that causes its victims to endure severe seizures at random, with the only cure being to watch someone laugh. One day, during Narumi's part time job, a young boy with a giant suitcase fleeing from three adults runs into him. The boy introduces himself as Masaru Saiga, the new owner of the famous Saiga Enterprises following his father's recent death. However, other members of his family are trying to assassinate him and claim the fortune for themselves. Determined to save the child, Narumi helps Masaru escape and ends up fighting the pursuers, only to discover that they are sentient humanoid puppets with superhuman strength. As Narumi is about to lose, a white-haired girl suddenly joins the fray and swiftly summons yet another puppet from the boy's suitcase, claiming herself to be Shirogane, Masaru's guardian. Karakuri Circus follows three people from different backgrounds whose fates intertwine and diverge as they unravel the mysteries of an ancient tale of love and betrayal, and the long, ancient battle between humans and puppets.