After Akihito Kanbara reunites with Mirai Kuriyama—whom he believed had vanished after defeating Beyond the Boundary—he discovers a heartbreaking fact: Mirai has lost all memory of him, their friends, and her past as a Spirit Warrior. Akihito is utterly devastated, but realizes that she has a unique opportunity. Mirai can finally live the life of a normal girl—where she'll be completely devoid of the supernatural society that both shunned and used her. While it's all for the sake of Mirai's happiness, the price is costly—Akihito and his friends must keep her true origins a secret from her, and as a result avoid befriending her.

However, the troubling memories of Mirai's old life gradually begin to resurface, and a mysterious new evil leads a group of shadow-like creatures into the city with the goal of seeking her out. As the situations become dire, Akihito must fight to protect himself, his closest friends, and Mirai—the bespectacled beauty he holds most dear.