After detective Natsumi Yukihira brings an end to the police hospital terrorist case, Natsumi is transferred to the Nishimonbetsu Police Station in Hokkaido. Meanwhile, a series of grotesque murders occurs in downtown Tokyo involving nails placed in the body of the victims. The fingerprint of Natsumi's ex-husband, freelancer journalist Kazuo Sato, is found on the the body of a victim and Kazuo is placed on the most wanted list. Soon after, Kazuo finds Natsumi and hands her a USB memory stick. The device contains information on a secret organization within the police department. Kazuo tells Natsumi that the series of murders are warnings and suspects become the next victims. Natsumi is then arrested as a suspect. Tokyo prosecutor Katsuaki Murakami appears at the Nishimonbetsu Police Station to investigate.

The story follows Akane, a girl with no self-confidence. On the day before her birthday, she meets a mysterious alchemist, Hippocrates, and his student, Pipo, who both tell her they're on a mission to save the world. Together, they set out from the basement for "Wonderland," and Akane finds herself labelled Wonderland's savior.