L’unidicenne Masaru Saiga eredita il patrimonio del padre morto in un incidente e diviene preda di misteriosi rapitori che mirano alla sua ricchezza. Il giovane Narumi Kato lo salva ma i rapitori tornano alla carica e si scopre che si tratta di bambole dalla forza sovraumana. Tutto sembra perduto quando appare una donna dai capelli d’argento: Shirogane

Dopo una brevissima pausa Masaru, Narumi e Shirogane vengono rintracciati e nuovamente assaliti. L’assassino Eiryo Ashihana attacca con il burattino Pulcinella, dalle fattezze di un clown. Shirogane risponde dispiegando il suo burattino Harlequin, ma in un momento di distrazione uno degli scagnozzi di Ashihana agguanta Masaru

Dopo aver resistito a numerosi attacchi, Masaru viene infine rapito e conddotto a Karuizawa. Per salvarlo, Narumi e Shirogane irrompono nella villa di Zenji Saiga, zio di Masaru e artefice del rapimento. Masaru sta per fuggire dalla villa, quando scopre alcuni misteriosi documenti appartenuti al padre ormai scomparso, Sadayoshi Saiga

Sfuggire a Zenji e smettere di piagnucolare: queste le decisioni di Masaru che, nel frattempo, incontra di nuovo il suo potenziale assassino Eiryo Ashihana. Anziché fuggire, però, gli propone un’alleanza. Intanto Narumi e Shirogane vengono catturati dai burattinai di Zenji e sembrano essere spacciati

Narumi, che ha più volte tirato fuori Masaru dai guai, rimane coinvolto nell’esplosione di villa Saiga e di lui non si hanno più notizie. Benché sovrastato dal sentimento di perdita, Masaru decide di essere forte come lui gli ha insegnato e torna a frequentare la scuola. Shirogane, per proteggerlo, si iscrive ad un liceo vicino.

Narumi, ritenuto morto dopo l’esplosione a Karuizawa, si risveglia in una stanza di ospedale. Lì conosce il seduttore Guy ed un’anziana donna di nome Lucille. Mentre lotta per recuperare la memoria, fa amicizia con i bambini ricoverati e capisce che sta succedendo qualcosa di strano quando nota che le sue ferite guariscono in maniera inaspettatamente veloce...

Narumi viene a conoscenza della sindrome ZONAPHA e della causa della sua diffusione: il Circo della Mezzanotte. Per garantire un futuro ai bambini deve annientare gli automi. Decide quindi di trasformarsi in uno "shirogane", un distruttore di automi. Nel frattempo Masaru e Shirogane si sono uniti al Circo Nakamachi, dove incontrano la misteriosa Vilma.

Il Circo Nakamachi sta per partire con un nuovo spettacolo a Izu, grazie ai fondi ottenuti e al nuovo numero della lanciatrice di coltelli Vilma. Contemporaneamente Narumi, Guy e Lucille si imbarcano su un volo diretto a Shangai, sulle tracce del Circo della Mezzanotte. Ma sullo stesso aereo ci sono anche gli automi e nei cieli dell'Oceano Pacifico ha inizio una feroce battaglia.

Guy viene ferito e cade in mare. Lo salva il gruppo del Circo Nakamachi e si scopre, con stupore, che è stato il maestro burattinaio di Shirogane. L'incontro porta Shirogane ad aprirsi con Masaru e Masaru, a sua volta, a partire per un viaggio solitario alla ricerca della sua infanzia. Anche Narumi e Lucille, giunti in Cina incontrano il loro maestro di Kenpo, Liang.

Liang narra la verità sul passato, sui fratelli aspiranti alchemisti Jin e Yin e sulla donna innamorata di entrambi, Francine. A causa della differenza di vedute tra i tre, in un villaggio della Francia ebbe origine la ZONAPHA, che avrebbe contagiato il mondo. Narumi e i suoi devono ancora riprendersi quando improvvisamente compare Pantalone, uno dei quattro automi più anziane.

In Maine, Shirogane-Os prepare to attack the Midnight Circus in the Sahara. Narumi, Lucille, and Ming-Xia join them, meeting George Laroche and Ashihana in France. At the circus, they face the Faceless Commander and his Shirogane-Os. Les Quatre Pionniers propose one-on-one battles. Zed destroys two automata but is defeated by Merry-Go-Round Olsen. Narumi smashes an automaton, while Fatima and Ming-Xia face Orazio and Pedrolino. After winning, a trapdoor sends them to another challenge.

Fatima and Ming-Xia receive treatment, while Narumi, Rockenfield, Malina, and Tor face deadly traps in the Midnight Circus. They split into two groups, with Narumi’s group navigating a dark staircase. The others enter a chamber requiring combat to proceed. George and Ashihana arrive by helicopter. Below, Narumi’s group faces more traps, and the Faceless Commander sacrifices himself to save Narumi, who reunites with Tor, Timbavati, Rockenfield, and Malina to confront Les Quatre Pionniers.

Tor, Timbavati, Rockenfield, and Malina battle the Quatre Pionniers. A weakened Narumi struggles to reach Doll Francine. Lucille arrives with Fatima, Ming-Xia, Ashihana, and George, unveiling her Francine marionette, Angelina, halting the circus. Lucille convinces Dottore to abandon Francine, but he fatally wounds her, causing her to crystallize. Tor self-destructs to eliminate automata, allowing Narumi’s treatment. Timbavati battles Columbine, using his Shirogane blood to neutralize her, but both die.

Pantalone and Arlecchino destroy the Francine marionette and George. A Shirogane doctor dies saving Narumi. Fatima’s Spinettina fails against Pantalone and Arlecchino, but Narumi defeats them. Lady Francine reveals she’s a copy, and the real Francine is elsewhere. Narumi attacks Shirogane, mistaking her for Francine based on a Clogue survivor’s claim, but spares her after recalling their past with Masaru.

At the Saiga ruins, Masaru receives a letter and keys from Sadayoshi, revealing he’s his father reborn. Kuroga puppeteers attack with Shogetsu, believing Masaru is Sadayoshi. Masaru uses Goyellemes and Captain Nemo to defeat them but is captured and brought before Shōji’s conscious remains.

Shōji forces Masaru to drink his blood, triggering memories of Shōji’s past at Miura Dojo and meeting Angelina (Tohno-dayu), who wielded Arlequin. Shōji drank Aqua Vitae to stay with her forever, vowing eternal love.

Shōji reveals Sadayoshi was adopted, not his biological son. Guy shares his Zonapha infection and transformation into a Shirogane. Angelina refused to surrender her Soft Stone, defeating Guy. Shōji adjusted a Francine automaton to be less powerful and brought her home to Angelina, who later gave birth to a daughter.

Shōji names his daughter Éléonore. Her birth affects Guy and Francine, who feels incomplete without a vital gear. Automata attack for the Soft Stone, now in Éléonore. Francine escapes with her, turning well water into Aqua Vitae, consuming herself. Angelina dies fighting automata, crystallizing. Shōji and Guy continue the battle.

Guy insists Masaru is Sadayoshi. Masaru denies it, encountering Éléonore but falling unconscious after Guy’s attack. Shōji’s memories reveal Éléonore’s life in Quiberon and Sadayoshi’s betrayal, using Masaru for immortality. Shōji destroyed the memory data, surviving Sadayoshi’s attempt to kill him.

Masaru recalls Sadayoshi downloading memories into him during a car crash, where Shōji and Guy intervened. At Karuizawa, Daiki, the Faceless Commander, claims to be Masaru’s father, embodying Bai Jin and Sadayoshi. He attacks, but Éléonore takes a blow meant for Masaru. Daiki escapes with her, challenging Masaru to follow. Shōji dies, reuniting with Angelina in the afterlife.

Masaru mourns Shōji as villagers succumb to Zonapha. The Faceless Commander, Deus, unleashes Artemis, composed of Apollyon bugs. Masaru and Guy pursue, but Cupidia downs Guy. Narumi destroys Cupidia and joins Guy to reach the Zonapha Research Institute, where Fou’s “Harry” can counter Apollyon. Faceless’ automata attack, and Arlecchino, Pantalone, and Colombine discover Éléonore resembles Francine.

Ming-Xia defeats Gambler Jones to save Tom. George calms children with music but faces Bola Misteriosa. Ashihana challenges Pantalone, who spares him, recalling Francine’s orders.

Ashihana uses George’s Shirogane blood to fight Pantalone, who spares him. George defeats Bola Misteriosa but dies. Narumi destroys automata, reaching Dr. Banhart’s lab with Ming-Xia, confronting Blom Blom Low and Drill September. Guy and Olympia hold off automata outside.

Narumi and Ming-Xia defeat Blom Blom Low and Drill September. Ashihana spares Pantalone, who helps Guy. The Long-legged Clown Express rescues survivors, including “Harry.” Masaru and Lise chase Faceless’s airship.

Masaru and Lise crash on Mont Saint-Michel. Aboard Faceless’s airship, Éléonore meets automata like Captain Graziano. On the island, Dr. Lao’s beasts attack, but Naya Steele helps Masaru after disabling Colombine. Masaru discovers the Shirogane-O’s human bodies.

Lise tames Dr. Lao’s beasts, killing him. Faceless beats Éléonore to possess Masaru. Colombine shows Masaru the Shirogane-O’s bodies. Naya attacks, but Masaru disables her. Faceless confronts Masaru with new automata.

Masaru fights Faceless’s automata with Harlequin. Lise and Colombine battle to stop Faceless’s rocket. Faceless tries to transfer his consciousness into Masaru but fails due to Masaru’s resistance.

Masaru resists Faceless’s control, using Éléonore’s blood. Colombine fights Diamantina’s teddy bears. Masaru frees Éléonore, leaving Faceless in the rocket. Narumi arrives, finding Colombine’s remains after her sacrifice.

Éléonore proves her loyalty by sharing Aqua Vitae with Zonapha sufferers. Faceless threatens to kill humanity with Apollyon. Fou plans to send “Harry” to stop him. Narumi mistrusts Éléonore.

Guy challenges Narumi over Éléonore but is dying. Masaru learns Narumi is alive and searches for him. The Nakamachi Circus heads to the launch pad with “Harry,” while Guy sacrifices himself to stop automata.

Vilma equips the Nakamachi Circus with Éléonore’s blood-tinted knives. Automata attack the train, and Vilma dies fighting Wild West Jane. Masaru destroys Keniss.

Shinobu consoles Masaru, revealing Éléonore’s sacrifices. The Nakamachi Trio prepares to fight Lady Spider and Captain Graziano. Arlequino and Pantalone seek Éléonore’s permission to stop Bringhella and Harlequin.

The Nakamachi Trio distracts Lady Spider with circus tricks, killing her with Vilma’s knife. Arlequino and Pantalone fight Bringhella and Harlequin, who confesses his love for Éléonore, tearing Pantalone apart.

Éléonore fights Harlequin to protect Narumi. Narumi defeats Bringhella. Masaru beats Captain Graziano. At the launch pad, Narumi and Masaru fight automata, with Masaru defending Narumi’s rear.

Masaru blinds Narumi to take his place in the shuttle. Narumi and Éléonore defeat Harlequin and declare their love. Ashihana dies stopping Pinball-K. Masaru confronts Faceless, who cloned Bai Jin’s body.

Faceless refuses Masaru’s plea for the Zonapha cure. Diamantina destroys Francine automata but is dismantled. Faceless helps redirect the crashing station, revealing Éléonore’s singing cures Zonapha. Masaru escapes, and humanity is saved. Six years later, Narumi and Éléonore’s circus brings joy to war-torn areas, and Masaru saves children in a bear suit.