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 Specialized Extracurricular Execution Squad (SEES), and with his new friends, confronts the threat of the Shadows.