The story begins when orphaned teenager Makoto Yuki transfers to Gekkoukan High School in Iwatodai City and discovers a phenomenon called the Dark Hour during which supernatural entities called Shadows roam freely. After awakening an ability within himself called Persona, Yuki finds himself intertwined in the ongoing struggle against the Shadows with his new schoolmates. In the process, Makoto and his friends unearth terrifying truths all the while unaware of the destiny which lies ahead.