Naoto Fuyumine is a swordswoman marked by short black hair, pale skin, and a distinctive X-shaped scar across her chest. This scar stems from the murder of her parents during childhood, a trauma that induced amnesia, erasing her memories and original name. Discovered and taken in by the swordsman Fuyumine, she trained under him while mistakenly believing him responsible for her parents' death. He named her "Naoto" after another individual. Years later, she found Fuyumine murdered by his other student, Magato, who revealed her parents were actually killed by the "original Naoto" from an underground organization. Honoring her mentor, she adopted his surname and inherited his black katana, "Dog Biter" (Inugami), embarking on a quest for vengeance against the original Naoto.

Her pursuit led her to collaborate with others, including the genetically modified gunman Heine Rammsteiner and information broker Badou Nails. Naoto and Heine initially clashed frequently over opposing ideals and methods; Heine employed brutal tactics while Naoto avoided lethal force where possible. Despite the tension, their combat styles proved complementary. They gradually formed a shaky mutual understanding, often partnering on missions. Naoto became one of the few women Heine tolerated physical contact with, aside from the genetically engineered girl Nill, whom Naoto rescued from a crime family, protected, and befriended.

Naoto's backstory grew more complex upon confronting Campanella Frühling, the "original Naoto." Frühling revealed Naoto was a genetically engineered clone designed as a vessel for the underground scientist Angelika Einstürzen. Her presumed parents were Einstürzen researchers who betrayed the organization and tried to escape with her, only to be killed by Frühling. This revelation tormented Naoto, suggesting Fuyumine might have known her origin. Heine helped her recover, strengthening their bond. They later made a pact to stop each other if mentally compromised by Einstürzen's influence, demonstrated when Heine resisted violent impulses after Naoto—briefly controlled by Einstürzen—stabbed him with her katana, a weapon lethal to those with Kerberos Spine implants like Heine.

Her katana's properties and combat skills proved vital against the underground organization. Though exceptionally agile and skilled, her reluctance to kill sometimes disadvantaged her in battle. As events unfolded, Naoto shifted from solitary vengeance to deeper alliances, pursuing Heine into the underground to confront their shared past. Frühling noted Naoto was not yet ready to defeat her, though Magato predicted she would eventually succeed.