Fadas possuem e residem dentro de animais, concedendo-lhes poderes especiais. Ao remover cirurgicamente e transplantar os órgãos de um animal possuído em um humano, os humanos podem parcialmente invocar a fada e usá-la como uma arma. Eventualmente, esses indivíduos foram usados para a guerra e foram chamados de "Soldados Fadas". Depois de uma longa guerra, esses soldados perderam seu propósito e tiveram que se reintegrar à sociedade. Nove anos após o fim da guerra, Maria é uma nova recruta de Dorothea, uma organização dedicada à investigação e repressão de crimes e incidentes relacionados com as fadas. Mesmo em tempos de paz, o governo ainda é instável. Muitos criminosos ainda guardam as feridas do conflito anterior, e há grupos terroristas empenhados em se vingar.
Marlya has been searching for Veronica ever since the great war, but Veronica seems to be conducting a search of her own. When the two of them, and Free, all run headlong into each other, it quickly escalates into a fairy-fueled fight.
Free and Marlya go on a mission to catch some mafia gangsters who are selling artificial fairies, and it's there that Free encounters his old war buddy Wolfran. But Wolf's working for the mafia now, so this time they won't be fighting on the same side.
Free and Marlya are dispatched to collect the Black Fairy Tome from a fairy scholar in Timoon, but they're not the only guests who show up. Every party has its own agenda, and the tome suddenly becomes the hot topic of the evening.
Free and Marlya manage to secure what is supposedly the Black Fairy Tome, but Sweetie isn't about to give up easily. It's not long before a pair of mafia agents are called in to clean up her mess, which leads to a battle beneath an old church.
Veronica shows up to help Marlya deal with Jonathan, while Free continues to battle Patty. Later on, Marlya gets to know some of the other Dorothea members better when they throw her a belated welcome party.
Dorothea tightens security throughout Rondacia as the anniversary of the war's end approaches. Between another supposed piece of the Black Fairy Tome surfacing, and one of the new-model artificial fairies malfunctioning, there's plenty of work to do.
More new artificial fairies malfunction, and suspicion grows that someone with military connections is sabotaging them. Sweetie brokers a deal with Dorothea in an effort to acquire the piece of the Black Fairy Tome that was recently sold at auction.
Sweetie and Dorothea both make their move against Gilbert Warlock, as the mystery surrounding the malfunctioning artificial fairies slowly unravels. Now it's up to Chase to figure out the culprit's identity, and what exactly they're trying to accomplish.
As a reward for saving the prime minister's life, the Duke of Hybranz asks for one of the seven Fairy Weapons. As Dorothea transports this powerful weapon to his duchy, the big question on everyone's mind is what he intends to do with it.
When a group from Dorothea goes to inspect the Duchy of Kal-o, Marlya comes face to face with Ray Dawn. She also questions her motivations when she goes to visit an old friend. Meanwhile, Liscar's violent conspiracy continues with its progress.
The Duchy of Hybranz announces its intention to break away from Unified Zesskia. As the Unified Forces and most of Dorothea set out to put down the rebellion, it turns out that Rondacia might actually be the true target for Diese, Arcame, and Liscar.
Free and Marlya lead their Dorothea contingent in an attempt to drive Liscar's forces out of the palace, as Diese's intrigue enters its end game. But Wolfran just might have a hidden agenda of his own. Could this be the end of Unified Zesskia?
As Rondacia recovers from the foiled attack, the tragedy of Suna is revealed in flashback. Marlya, Veronica, and Ray are all from that village, and their lives are interconnected not only with one another, but with the fairies that once lived there.
Dorothea members are escorting Ray Dawn back to Kal-o when a bridge is sabotaged. Forced to stay the night in an old abandoned castle, they come under attack both by some artificial fairies and by Veronica, in her attempt to assassinate Ray.
Dorothea sets out to round up and interrogate as many Arcame members as they can find in Rondacia, and clues point to Christoph Rahn's involvement in Diese's rebellion. Meanwhile, both Marlya and Free are having trouble dealing with personal issues.
A chapter of the Black Fairy Tome turns up at the port island city of Baleun, and multiple parties converge there in an attempt to claim it. Newly formed alliances prove to be fluid and unpredictable, as various secrets begin to come to light.
Damien confesses to Dorothea about his identify and his ties to Veronica, along with information on the Black Fairy Tome. Based on information provided by Sweetie, Dorothea begins rounding up members of Gui Carlin in an effort to gather more tome pieces.
Suspicions about the Ministry of Fairies grow as Dorothea launches a raid on Eajey's hideout. Gui Carlin might be on its last legs, but there are other, potentially more dangerous groups that want the Black Fairy Tome for their own ends.
It comes to light that the Marco Bellwood might have nefarious purposes for acquiring the last pieces of the Black Fairy Tome, as Marlya gradually learns more about how different her situation is from that of other Fairy Soldiers.
Bellwood and most of the Eins Order go into hiding, and a massive manhunt is launched to track them down. Marlya and Free locate someone from Marlya's past, but the news he tells them only makes the whole situation that much more alarming.
With the prime minister dead, Ray Dawn comes to Rondacia. Veronica is presumably close behind, meaning all three of the fairy-possessed are now in one place. Marlya desperately tries to locate Veronica before the order can complete its horrific plan.
The Eins Order launches an attack just prior to Golbarn's funeral. This results in most everyone in Dorothea being split up, and with Ray Dawn badly injured. Once Marlya is left by herself to guard Ray, Veronica chooses that time to exact her revenge.
Various battles are fought throughout Rondacia, as the revived Divine Beast slowly makes its way into the city, laying waste to everything in its path. It slowly dawns on Marlya that she might be the one who can put a stop to the lumbering catastrophe.
Free and Wolfran fight to put an end to Griff Mercer's ambition and what's left of the fanatical Eins Order. Meanwhile, Marlya and Veronica join forces directly against the Divine Beast. But how can something so overwhelmingly powerful be stopped?
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