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.
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 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.
As Masaru visits the ruins of his family home in Karuizawa, he recalls past; from the time his mother died to the assassination attempts when he met Shirogane and Narumi. He is greeted by the caretaker who gives him a letter and a set of keys to an underground room, left by Sadayoshi Saiga 30 years ago. Masaru opens the room which triggers a recording telling Masaru that the room has been left in case the memory transfer failed and informs Masaru that he is in fact his father reborn. He exits the room and is attacked by puppeteers of Kuroga village with the ninja marionette, Shogetsu, believing him to be Sadayoshi. Masaru retreats, and with the assistance of Gryphon, he activates the massive marionette, Goyellemes and defeats Shogetsu. The Kuroga attack again with another marionette, but Mararu counters with the lighter Captain Nemo and slices it to pieces. Masaru then activate the third marionette and tries to escape, but is captured by the Kuroga and brought before the remains of his grandfather which appears to be still conscious.
Shōji tells Masaru that Sadayoshi was not his son, and that he and Angelina started to create their own marionettes. The shirogane, Dean Maistre arrived to pick up the marionettes for Lucille, and they later adopted Dean as their son, naming him Sadayoshi. However some time later, Angelina became pregnant. Back in the present, Guy arrives at the underground room and tells Masaru the story of how he contracted Zonapha and was abandoned by his mother and how Lucille turned him into a shirogane. Years later, Lucille sent him on a mission to see Angelina at Kuroga village and extract her "Soft Stone" to convert Zonapha sufferers into shirogane. Angelina refused to give up the stone and used Arlequin to fight Guy's Olympia, defeating him, but then welcomed him into her household. Then, another Shōji memory shows Masaru how Shōji encountered the Francine automaton whose creator abandoned her because she could not laugh. Shōji adjusted her to make her less powerful and took her home to meet Angelina who welcomed her. Shortly thereafter, Angelina gave birth to Éléonore.
Following revelations of the past, Guy again asserts that Masaru is Sadayoshi. Masaru denies it and runs off and encounters Éléonore Shirogane, but he is attacked by Guy and falls down a cliff unconscious. Masaru then recalls the memories of Shōji, from the saving of Éléonore and her life in the Quiberon orphanage under the care and training of Lucille. Then the betrayal of Sadayoshi by using his son Masaru as a vehicle for his memories so that he could essentially become immortal. However, Shōji was already prepared and destroyed the memory data back at Karuizawa causing Sadayoshi to try to kill him. Shōji survived but it was announced that he had died to protect him from Sadayoshi. Meanwhile, Sadayoshi sent Éléonore to join a circus to keep her away from Masaru.
Masaru admits that he now understands more of his past and recalls that on the night of his father's death, he collapsed after drinking cocoa. As Sadayoshi drove from Karuizawa, downloading his memories into the unconscious Masaru, he encountered Shōji on the road. While Shōji who attacked him, Guy and the Shirogane saved Masaru. As the car crashed, Shōji and Sadayoshi were flipped into a bath of acid, killing Sadayoshi and badly damaging Shōji. Back in the present at Karuizawa, just as Guy prepares to kill Masaru, Daiki reveals himself to be the Faceless Commander and claims that Masauru is his son. He explains how he is the reincarnation of both Bai Jin and Sadayoshi Saiga, and he attacks Guy and Shōji. Appearing like a powerful dark sun, he then prepares to take Masaru who valiantly fights back, however Éléonore suddenly appears and takes a blow meant for Masaru. The Faceless Commander then escapes to a waiting airship, taking Éléonore and Arleqiuin with him, challenging Masaru to follow him. Meanwhile, Shōji's remaining body crystallizes as he dies in Masaru's arms. In the afterlife, Shōji encounters Angelinga who has been waiting for him since her death, and they keep their promise to spend eternity together.
After defeating Pantalone, Harlequin closes in on the train carrying Narumi and Éléonore. Narumi immediately squares up to him, but Éléonore steps between them. Armed with Arlequin, she engages Harlequin in a duel in order to protect Narumi. Meanwhile, Masaru is involved in his own airborne duel with Graziano.