Every night when the clock strikes midnight, a phenomenon called "The Dark Hour" occurs. During this "hidden" hour of the day, normal humans are transmogrified into coffin-like objects, unaware of the world around them. What's more, evil creatures called Shadows appear to prey on the minds of humans, inflicting a zombie-like condition commonly known as Apathy Syndrome.

You are a New Transfer Student moving to Tatsumi Port Island to attend Gekkoukan High School. Soon after settling into your new dormitory, you are discovered to have "the potential": the ability to remain as a human within the Dark Hour, and to fight the Shadows with a mysterious inner-power called "Persona". Recruited into the Specialized Extracurricular Execution Squad (SEES), a secret student society dedicated to fighting the Shadows, you now have to balance your school life, your social life and your new demon-hunting life.