Narumi Katou is an elderly man who suffers from ZONAPHA Syndrome, an obscure illness that manifests in abrupt and violent seizures only quenched by witnessing someone laughing. During his part-time job, Narumi meets Masaru Saiga, a young boy targeted by three pursuers. Masaru discloses that he's inherited Saiga Enterprises after his father's death, but his avaricious relatives want to take the fortune for themselves. Determined to shield Masaru, Narumi fights the attackers, learning that they're not humans but sentient marionettes with exceptional strength. Despite his resolute efforts, Narumi is outnumbered and overpowered until he's joined by Shirogane, a fierce girl possessing ivory hair who's Masaru's protector. With a fresh puppet from Masaru's suitcase, Shirogane enters the fray, and together they defeat the assailants. Karakuri Circus chronicles the lives of three individuals with different backgrounds whose destinies interweave and diverge as they unveil an ancient narrative of love and betrayal, and an ongoing conflict between people and puppets.