After inheriting the family fortune, eleven-year-old Masaru Saiga is targeted by kidnappers armed with bizarre and deadly puppets. He escapes once aided by circus employee Narumi Kato, but the kidnappers soon catch up with them. Just when all seems lost, the two are saved by the mysterious Shirogane who wields her own marionette. From then on, the trio’s fates become inexorably intertwined...
Eleven-year-old Masaru Saiga inherited a vast fortune after his father died in an accident. These riches make Masaru a target for kidnappers, who send fearsome puppets to abduct him. Masaru escapes with the help of circus employee Narumi Kato, but the kidnappers soon catch up with them. All seems lost until a mysterious woman named Shirogane appears.
After the briefest of respites, Masaru, Narumi and Shirogane are plunged into peril once more. Assassin Eiryo Ashihana has tracked them down and attacks with the evil clown-like marionette Pulcinella. Shirogane unleashes her own marionette Arlequin in response, but while she is distracted, Ashihana’s henchmen seize Masaru.
The kidnappers relentless attacks finally succeed and they snatch Masaru. Narumi and Shirogane discover that Masaru’s uncle, Zenji Saiga, is the mastermind behind the abduction, and they rush to his mansion to attempt a rescue. Masaru, meanwhile, tries to make his own escape, but in doing so stumbles across a shocking file written by his late father.
Masaru determines that overcoming his own weakness is the only way he will escape from his uncle Zenji. He comes face to face once more with his would-be assassin Ashihana, but chooses not to run and makes Ashihana a counter-offer to work for him instead. While attempting to rescue Masaru, Narumi and Shirogane are themselves captured by Zenji’s puppeteers and seem to have no way out...
After having rescued Masaru numerous times, Narumi got caught in the blast that destroyed Zenji’s mansion and has not been seen since. Masaru’s sense of loss is profound, but he is determined to be strong as Narumi had taught him. He decides to go back to school in an effort to return to a normal life. Shirogane also enrolls in the adjacent high school so she can continue to watch over Masaru.
Narumi, despite being presumed dead after the explosion in Karuizawa, awakens to find himself in a hospital. There he meets ladies' man Guy and an old woman named Lucille and struggles to regain his memory of what happened. As Narumi interacts with the hospital’s child patients and witnesses his own wounds healing with incredible speed, he begins to suspect that something strange is going on.
Having learned the truth about ZONAPHA syndrome, Narumi realizes there is only one way he can give children who suffer from it a chance of a future. He must destroy the automata the Midnight Circus uses to spread the disease. To do so he resolves to become a “shirogane” – a destroyer of automata. Meanwhile, Masaru and Shirogane have joined the Nakamachi Circus and encounter the mysterious Vilma.
With their numbers boosted by the addition of knife-thrower Vilma and their coffers swelled by successful fundraising, Nakamachi Circus are ready to put on a show in Izu. As they prepare for opening night, Narumi, Guy and Lucille board a plane for Shanghai on the trail of the Midnight Circus. However, several automata are also on board and a fierce fight breaks out high above the Pacific Ocean.
The members of Nakamachi Circus rescue the injured Guy, who turns out to be Shirogane’s marionette teacher. This unexpected reunion leads Shirogane to open up about her past to Masaru, who in turn sets out alone on a journey to solve the mysteries surrounding his own upbringing. Narumi also reunites with a figure from his past as he and Lucille meet his old martial arts master, Liang, in China.
Liang recounts the tale of the love triangle that lead to the birth of ZONAPHA syndrome. Brothers and aspiring alchemists Jin and Yin both fell in love with the same woman, Francine, and their rivalry unleashed the tragedy that would overtake the world. Narumi and his companions are still reacting to learning this terrible truth when Pantalone, one of the four oldest automata, appears before them.