Based on the PlayStation 2 game of the same name. A teenager who was orphaned as a young boy returns to the city of his childhood. Shortly after transferring to Gekkoukan High School, he is attacked by Shadows — creatures that feed on the minds of their victims. He soon discovers that he shares a special ability with other students at his new school. From them, he learns of the “Dark Hour,” a hidden time that exists between one day and the next, swarming with Shadows. He joins the Special Extracurricular Execute Sector (SEES), and with his new friends, confronts the threat of the Shadows.

2011, Seta Souji moves to the countryside to his uncle's house due to his parents working abroad. Not very friendly, he however managed to make a few friends there, and they all decide to solve the mystery behind the sudden cases of serial murders that strikes the area.