"Fairy Gone" is set in a world where fairies, once wild and untamed, have been captured and integrated into human bodies to create powerful soldiers known as Fairy Soldiers. These soldiers were instrumental in ending a long-standing war, but their existence has left a lasting impact on society. The story unfolds in two timelines: one during the war and the other nine years after its conclusion, exploring the consequences of using fairies as weapons.

The narrative centers on Marlya Noel, a young woman who becomes a member of Dorothea, an organization tasked with investigating illegal fairy usage and maintaining order in the post-war world. Marlya’s personal journey is intertwined with her search for her childhood friend, Veronica Thorn, who has joined a rogue group called Ray Dawn. Ray Dawn seeks to dismantle the remnants of the war’s power structures, often resorting to violent means. As Marlya delves deeper into her mission, she uncovers secrets about her own past, including her connection to fairies and the true nature of the war.

The series features a diverse cast of characters, including Free Underbar, a skilled investigator with a mysterious past, and Klara Jindrich, a former soldier grappling with the moral implications of her actions during the war. The interactions between these characters highlight the complexities of loyalty, justice, and the ethical dilemmas surrounding the use of fairies as tools of war.

The plot is driven by political intrigue, as various factions vie for control over the remaining fairy soldiers and the power they wield. The story examines themes of identity, the cost of war, and the struggle for redemption in a world still haunted by its violent history. Through its dual timelines, "Fairy Gone" provides a layered exploration of how past actions shape the present, offering a nuanced portrayal of its characters and their motivations.