At St. Hermelin High School, a fortune-telling parlor game called Persona sets off a chain of events that cannot be undone. Playing it with a group of classmates, the protagonist loses consciousness and encounters Philemon — a being who grants the power of Persona and warns it will soon be needed. When the group visits their hospitalized classmate Maki Sonomura, the ICU vanishes and demons flood into the city: manifestations of humanity's inner darkness, drawn out by a reality-warping machine called the Deva System, built by the ruthless Takahisa Kandori. The story then divides into two routes.
In the SEBEC route, the protagonist pursues Kandori directly and eventually enters a duplicate version of the city created unconsciously by Maki's fractured mind. The Maki who has been traveling with the group is an idealized projection — the real Maki is trapped deeper inside herself, in a place called the Sea of Souls. Kandori's ambition to become divine ends in his possession by his own Persona, Nyarlathotep, then his death. But saving Maki requires confronting every piece of her shattered self, including the destructive Pandora, who wants to use the Deva System to erase everything.
The alternate Snow Queen route begins with a theater mask used to perform the Snow Queen play — nearly every student who wore it has died, except Saeko, whose friend disappeared instead. When the mask is found and Saeko puts it on, the town freezes. Three towers appear, guarded by the spirits of prior victims, and the only tool capable of freeing Saeko is the Demon Mirror. Behind the haunting is former classmate Tomomi Fujimori, a victim herself — now a vessel for the Night Queen Asura, who intends to cloak the world in permanent darkness.