The setting is Ayanagi City, located near the Sea of Japan. It is a futuristic metropolis constructed to facilitate recovery from the disaster caused by "Apathy Syndrome" ten years prior. High school student Shin Kanzato and his younger brother Jun reunite with their older brother Ryou, the chief of the Ayanagi City Police, after a decade apart. During this time, a series of bizarre incidents occur in Ayanagi City, including the sudden disappearance of a submarine crew while aboard their vessel, the resurgence of spiritless symptoms disturbing the world after ten years, and the case of an inside-out corpse where a student assumed a cruel appearance. Ryou investigates the organization behind this string of incidents, and Shin, having become entangled in the events, awakens his "Persona."