The player uses weapons and magical abilities gained by the use of "Personas" to defeat foes in a turn-based combat system. An iconic feature of the game is the method by which the members of SEES release their Personas: by firing an Evoker, a gun-like object, at their head, which does no damage but causes sufficient emotional stress to cause the Persona to appear. In addition to typical RPG elements, the game includes elements of dating simulation games as the player character progresses day by day through a school year, making friends and relationships that improve the strength of his Personas in battle.
The Main Character, 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; 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.
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 twelve Major Arcana of the Tarot. The group is told by Shuji Ikutsuki, the adult supervisor of the group, that defeating all the major Shadows will end the Dark Hour.