At Yasogami High School in Inaba, where a culture festival is being held, a strange bell rings, trapping the Investigation Team inside the school. Meanwhile, the members of the Specialized Extracurricular Execution Squad (SEES), find themselves transported to the Velvet Room elevator, which suddenly
winds up at Yasogami as well. Discovering a labyrinth hidden below the school, the two groups meet up and explore the area, fighting "shadows" along the way, in order to regain the memories of new characters Zen and Rei, which the characters believe will lead them to freedom. The dialogue and events vary depending on the player's choice to follow either the team of characters from Persona 3 or Persona 4.