A teenager who was orphaned as a young boy returns to the city of his childhood. Shortly after transferring to Gekkoukan High School, he is attacked by Shadows—creatures that feed on the minds of their victims. The assault awakens his Persona, Orpheus, his only chance at defeating these creatures of the night. He soon discovers that he shares this special ability with other students at his new school. From them he learns of the "Dark Hour," a hidden time that exists between one day and the next, swarming with Shadows. He joins the Specialized Extracurricular Execution Squad (SEES), and with his new friends, confronts the threat of the Shadows.

After signing a contract in which he "accepts his fate of his own free will," the main character battles with the other members of SEES against the Greater Shadows, incarnations with traits and appearances similar to those of the first 12 Major Arcana of the Tarot. While this is occurring, he continues to encounter and eventually befriends the child who gave him the contract to sign at the very beginning of the game, an entity who refers to himself as Pharos, and is really the incarnation of Death, the 13th Arcana.