The game starts with the protagonist, along with schoolmates Hidehiko "Brown" Uesugi, Yuka Ayase and Masao "Mark" Inaba, playing a fortune-telling parlor game called "Persona" while Kei Nanjō and Yukino Mayuzumi watch. After playing the game, the group see a ghostly figure, and the protagonist, Mark, Nanjō, and Yukino are rendered unconscious. The protagonist is then drawn into the realm of Philemon, who grants him the power of Persona and warns him that his new power will soon be needed. After the four recover and at the suggestion of their teacher Saeko, they go to have a check-up and visit classmate Maki Sonomura at the hospital. While visiting, Maki is taken ill, and while they are waiting for news, the ICU where Maki is being treated vanishes and the town is attacked by demons, the summoned manifestations of people's inner darkness. Using their Personas, the four defend themselves, and after meeting up with Eriko "Elly" Kirishima, they head to the town's Ayama Shrine to find Maki's mother Setsuko. Upon arrival, they find Setsuko wounded after an attack by Takahisa Kandori. Setsuko reveals him to be the culprit behind the changes to the town, caused by a reality-altering machine called the Deva System. Nanjō and Mark head out to confront SEBEC, while the protagonist, Elly and Yukino bring Setsuko back to the school. After this point, the game splits into two story routes: the main SEBEC route, and the alternate Snow Queen route.
In the SEBEC route, should the protagonist decide to confront SEBEC, he is first joined by an apparently-recovered Maki, then asked by Nanjō to help save Mark, who is captured by demons. The protagonist, Maki and Nanjō rescue Mark, but on the way Maki displays an odd lack of certain memories including being hospitalized. After rescuing Mark and infiltrating SEBEC, the group confront Kandori. After cornering him inside the Deva System, a girl in black called Aki appears and knocks the party unconscious. When they awake, they find themselves in a duplicate, idealized version of their world. The group eventually find and corner Kandori, whose ultimate goal was to become a deity and find meaning in life. After an initial fight, Kandori is possessed by his Persona Nyarlathotep, then finally defeated. Before dying, Kandori reveals that the Maki who has been traveling with the party is the "Ideal Maki", a version of herself from the true Maki's heart. Aki and a girl in white called Mai are also pieces of Maki, and the idealized Mikage-cho was created by Maki, and brought into reality when she unexpectedly linked with the Deva System. The group must help Maki avoid Kandori's path towards isolation and his current actions. The group manage to convince Ideal Maki to overlook her original self's unconscious actions and join them in fixing the problem. After rescuing the true Maki's self from the Sea of Souls, where all human life begins, the group must then confront Pandora, an aspect of Maki that wants to use the Deva System to destroy everything. When Pandora is defeated, all the pieces of Maki merge back into one, reversing the effects on the town and restoring her to full health. Philemon meets with the group and congratulates them on their success.
The Snow Queen route, which takes place in the town of Mikage-cho, is unlocked by investigating an urban legend within the school surrounding a theatrical mask used in performances of "The Snow Queen": nearly everyone who wears the mask to play the title role has died, with the exception of Saeko, whose friend disappeared instead. After finding the mask, the protagonist encounters Saeko, who puts on the mask and is possessed by a spirit within it. Freezing the entire town, the possessed Saeko generates three towers, with the spirits of those previously killed by the mask as their guardians, whilst setting up her Ice Castle within the high school. Along with Yukino, Ayase, Elly, Brown, and Nanjō, the protagonist heads out to save Saeko. Philemon contacts them and tells them that the only way to save Saeko is the Demon Mirror, which can remove the source of the mask's curse. The spirit possessing Saeko turns out to be former classmate Tomomi Fujimori, who was horribly disfigured by the mask when she wore it in place of Saeko. Using the mirror, the group are able to free Saeko and bring Tomomi peace. It is then revealed that Tomomi herself was controlled by the Night Queen Asura, a powerful entity who wants to cloak the world in darkness. Upon defeating the Night Queen, the town is freed from her power.
