Schlimme Monster lauern in der Finsternis und warten darauf, dass Menschen in die verstecke Stunde gezogen werden, welche während Mitternacht stattfindet. Ein geheimer Schul-Club mit dem Namen SEES verteidigt die Menschheit vor Gefahren, während sie daran arbeiten, das Geheimnis der dunklen Stunde zu lüften.
Makoto Yuki - Minato Arisato is an orphaned teenager who transfers to Gekkoukan High School at Tatsumi Port Island and much to his confusion, finds himself experiencing strange phenomenon on his way to the dorm. Arriving at the Minatodai Dormitory, Makoto is greeted by a boy named Pharos and signed a contract the boy has prepared, before confronted by Yukari Takeba and Mitsuru Kirijo. The next day, on his first day in Gekkoukan High School, he befriends one of his classmates, Junpei Iori. The following night, Makoto dreams about a mysterious man named Igor with his assistant, Elizabeth, in a room called Velvet Room who are telling him of the journey he will face. Meanwhile, Mitsuru, Yukari, and the chairman of the school, Shuji Ikutsuki, observing Makoto from the command room, the Minatodai Dormitory comes under the attack of terrifying creatures called Shadow, injuring one of their team members, Akihiko Sanada. While Mitsuru and Akihiko fend off the Shadows downstairs, Yukari and Makoto are cornered by a gigantic one once they arrived there. In the nick of time, Makoto awakens to the power of his Persona, Orpheus, that then turns into Thanatos, easily defeating the Shadow. After recovering, Makoto finds out there exists a hidden period of time between one day and the next known as the Dark Hour. During this phenomenon time itself seems to come to a halt and unbeknownst to humanity, their bodies become transmogrified into coffins while Shadows roam freely. Only those who have awakened the power of Persona can experience the Dark Hour and stand any chance of stopping the Shadows. They invite him to join 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, which Makoto immediately accepts simply because he was asked to. Not long afterwards, Akihiko also recruits Junpei into their team and brings them to their school that turns into Shadow's nest during Dar
