The Main Character is a teenager who was orphaned as a young boy that 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; each is armed with an Evoker, a special handgun that they fire at their heads that does not harm them physically but causes emotional stress in order to summon forth their own Persona.

The Main Character learns that he is unique among the other members, being able to use multiple Personas and that he is guided by the formation of Social Links to improve his power. 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 by exploring Tartarus, a huge, chaotic tower that appears in the place of their school every Dark Hour.