Favaro Leone es un cazarrecompensas que viaja por el mundo cazando a los peores criminales. Siempre es perseguido por Kaisar Lidfard, el cual parece tener algún asunto pendiente con Favaro. Sin embargo, todo cambia cuando Favaro conoce a una misteriosa chica, que le pide que la lleve a una peligrosa ciudad al norte de Mistarcia.

Favaro intenta por todos los medios deshacerse de la cola de demonio que la chica, llamada Amira, le ha impuesto por contrato. Para ello, no dudará en conspirar contra la vida de la joven. Mientras, los dioses, que han descubierto el robo de la Llave de Dios, envían a los Caballeros de Orleans, comandados por Juana de Arco, en busca de Amira.

Después del robo de la llave, el mundo empieza a cambiar, presagios de lo que está por llegar. Siguiendo la pista de Favaro, Kaisar sufre un accidente y es salvado por una niña, que le lleva a un pequeño pueblecito. Pero no todo es lo que parece y menos en la niebla...

Los demonios mueven ficha y cada vez están más cerca de Amira. Favaro busca un barco que los lleve a Helheim y por su parte, Kaisar comienza a viajar con la niña de Nebelville, llamada Rita y que resulta ser una zombie. Favaro se encuentra con un viejo amigo de su padre, que resulta ser el capitán del barco que le puede llevar a Helheim.

Kaisar y Amira son secuestrados por Azazel, el líder de los demonios. En un intento por conseguir información, Amira es torturada sin éxito. Por su parte, Rita y Favaro buscan la ayuda de Bacchus para encontrar una forma de entrar en el castillo volador de Azazel.

Azazel asedia Anatae con la intención de hacerse con la Llave de Dios. Mientras la batalla entre humanos y demonios se intensifica, Amira se encuentra feliz al haberse encontrado con su padre en el interior del castillo. Mientras Favaro, Kaisar y Rita intentan sin éxito poner a salvo a Amira, Azazel aparece ante ellos.

El grupo es conducido ante el Rey Charioce, que ante la sorpresa de todos convierte en caballeros a Favaro y Kaiser. Amira identifica al lugarteniente de Juana de Arco, el capitán Lavallée, cómo su padre e insiste en verle. Juana es bendecida por los dioses con una espada sagrada, lo que despierta celos en Charioce y los demonios lo aprovechan para manipular su mente. Mientras, comienza a forjarse una traición entre los demonios.

Amira and Favaro slip out of the city while Rita causes a diversion and Lavalley tasks Kaisar to track them down in order to aid them in his stead. Back in the Capital Jeanne is framed by an unknown demon for attempted murder on the king as well as slaughtering of guards and the officer Gaurin. The Angels continue to fight to maintain the seal on Bahamut as it grows increasingly unstable. Kaisar catches up to Amira and Favaro in a forest where they are transported to an alternate space and free an imprisoned dragon when they remove a poisonous barb of Bahamut from his foot. The dragon reveals that when Amira's key meets the seal Bahamut will released, as it has been countless times before. Meanwhile the god clan and demon clan accuse the other of plotting against them and amass their forces to crush the other. Amira cries when she learns the world will end because of her, meaning her mother's death though Favaro resolves to change fate after enduring a vision of Bahamut and recalling his father's words. The King orders the death of Jeanne by burning at the stake and commands Lavalley to capture and kill any of her supporters while beneath the castle Rita investigates the cause of madness and trickery. The trio arrive in Prudisia while Favaro is troubled by what the dragon told him: Should Amira ever be close to Bahamut, she'll fuse with it permanently due to her god and demon blood as only a human vessel can maintain the seal; only the way to prevent the fusing is to kill Amira.

Rita escapes from the castle after being confronted by a suspicious cloaked man who threatens to dispose of her. Meanwhile the King proceeds with Jeanne D'Arc's death sentence for deceit and conspiracy carried out before a crowd of protesters who proclaim her innocence. As Jeanne burns she faces fiery visions of the gods forsaking her, including her patron angel, causing her to accept the words of the cloaked demon. Jeanne is converted from a saint into a witch by the demon and she escapes the capital by wielding a fierce and dark power as she is now a demon. Meanwhile Favaro thinks over the dragon's words of killing Amira as the trio continues their journey to find Amira's mother. They are intercepted by the cloaked man who is the same demon who tricked the king as well as Jeanne; Amira reveals him to be her mentor Martinet who in turn tells them they are in Helheim. Rita seeks out Bacchus and inquires about Martinet but the two run into a severely injured Azazel. The demon lord Beelzebub appears before the trio, capturing Kaisar and Favaro, telling Amira to fulfill her purpose before showing her mother. Martinet reveals in actually Beezlebub recreated Amira from Nicole as an imitation vessel and he is her "true" birth parent as all Amira's memories are fabricated since as she is a mere tool to release Bahamut. Amira's compromised emotional state causes the key's seal to unlock, falling into the demon's hands as the completed Transcendent Key. Azazel agrees to help Rita if she takes him to Abos while Favaro pretends to join the demons but Martient sees through the plan and forcibly makes Favaro a demon.

With Favaro transformed into a demon, he is now under their control. Beezlebub and Martient prepare Amira for transportation but not before blasting Kaisar away to fall into the depths below. The god clan attempt to maintain the seal on Bahamut but sense the presence of the Transcendent Key now that it is formed. Meanwhile Azazel converses with Rita and Bacchus, revealing that Beezlebub is the one behind Amira's actions as well Martinet; Rita theorizes Martient is not a demon like Beezlebub. While protecting the seal the angels are attacked by the corrupted Jeanne who slays Raphael and Uriel before going after Michael. Kaisar is saved by Bacchus in his flying carriage only to be attacked by Jeanne. While Bacchus fights Jeanne, Rita gives Kaisar a cure she made for the demon transformation and he taunts Azazel into helping him. Rita attempts to administer the last of the antidotes to Jeanne but fails only for Michael to successfully give it to Jeanne through a kiss after she impales him. Jeanne is freed, turning back into a saint while Michael's physical form disappears and he reassures her the world needs her. As Beezlebub prepares to destroy the angels protecting Bahamut's barrier Azazel attacks him and engages in battle for revenge. Kaisar duels with the demonic Favaro and upon seeing how he's become a true demon shoots him in the chest. Amira emerges from the Transcendent Key's orb, now with angel's wings. Lavalley appears before Kaisar, only for Rita to warn to get way from the knight. With the barrier fallen Bahamut beings to absorb Amira while everyone looks on helplessly; as Kaisar watches in disbelief Lavalley shoves him over the edge of the flying fortress before reveling in Bahamut's awakening.

Beelzebub declares the war between demons and gods over with Bahamut's awakening as he is its master, and commands the gods to bow before him. He then orders the great dragon to unleash its power to which it attacks Beelzebub before proceeding to blast everything in sight. Rita manages to save Kaisar and reveals that Lavalley is really, Gilles de Rais, a sorcerer with a bounty who is the one behind Bahamut's revival as well as all the deception. The demons and gods team up to fight against the uncontrollable Bahamut. Kaisar attempts to attack Lavalley only to find they have no effect before Lavalley reveals he is Martient as well. Elsewhere a heavily wounded Beelzebub curses Martient's deception of using Amira to be able control Bahamut before Azazel finishes him off, ending his revenge. A bloody Favaro appears, revealing he's not dead and begins combat against Kaisar seemingly by Lavalley's command. Favaro gains the upper hand before proceeding to cut Kaisar's hand off, presenting it with the bounty armband to Lavalley. Favaro catches Lavalley off guard by warning him about having a bounty on his head before Kaidar recites the bounty armband's incantation thus turning Lavalley into a bounty tablet. As Rita tends to Kaisar's wounds Favaro reveals that Kaisar managed to shoot him with the antidote, turning him back to normal and the fight was an act. As Bahamut continues to rage Favaro declares it's up to him to stop it and he'll kill Amira as it's the only way to stop the beast as well free her from sadness. Kaisar decides to join Favaro to save Amira, still believing there is a chance to separate her from Bahamut. In order keep Bahamut still for a minute the demons and gods work together to contain the beast to allow Favaro and Kaisar to approach it. With tears in his eyes Favaro screams Amira's name as he stabs Bahamut, unleashing a beam of light. Amira then appears before him, chiding him for being late and he promises to take her somewhere better than Helheim. Amira proceeds to kiss Favaro after realizing he isn't lying when he meets her with a serious, sincere gaze. She thanks Favaro before disappearing back inside Bahamut, causing the beast to explode though Kaisar escapes, leaving Favaro to be caught up in the blast that destroys his leg. Half a year later in the royal capital Kaisar, given a mechanical hand from Rita, commands the soldiers as a lieutenant with his knighthood intact. Favaro is alive with a mechanical right leg and is back to bounty hunting though he remarks Bahamut will never be forever gone. Kaisar then suddenly appears, forsaking his knightly duties, swearing not to be in Favaro's debt and the two ride off.