There is a hidden period of time between one day and the next known as "The Dark Hour". During this period, time itself seems to freeze and unbeknownst to humanity, their bodies become transmogrified into coffins while terrifying monsters called "Shadows" roam freely. Only those who have awakened to a special power called "Persona" can experience the Dark Hour and stand any chance of stopping the Shadows.
Makoto Yūki is an orphaned teenager who transfers to Gekkoukan High School at Tatsumi Port Island and much to his confusion, finds himself experiencing the Dark Hour upon arrival. When his new residence at the Minatodai Dormitory comes under the attack of a giant Shadow, Makoto inexplicably awakens to the power of Persona and aids in repelling the threat. After learning that his new Minatodai dormmates also possess the power of summoning Personas, they invite him to join and lead a covert club at Gekkoukan High called the Specialized Extracurricular Execution Squad - S.E.E.S. whose members have but one goal: to rid the world of the Shadows.