The story takes place in the Japanese city of Tatsumi Port Island, home to Gekkoukan High School. Unknown to most of its residents, a hidden period called the Dark Hour lurks between one day and the next. During this eerie time, ordinary people are transformed into coffins and left unaware, while reality itself warps: the high school twists into a towering labyrinth known as Tartarus, prowled by monstrous beings called Shadows that prey upon the minds of those who remain conscious. A group of students, able to withstand the Dark Hour, have formed the Specialized Extracurricular Execution Squad, or SEES, to investigate these phenomena. Wielding the power to summon manifestations of their inner selves called Personas, they battle the Shadows, and a newly arrived transfer student soon finds himself drawn into their dangerous nightly struggle.