At Gekkoukan High School, the Specialized Extracurricular Execution Squad, also known as S.E.E.S, is a peculiar after-school club. No matter the circumstances, the group does not falter from its responsibilities in combating the time anomaly called the Dark Hour. During this period, these select few remain awake and can summon Personas to fight Shadows tirelessly and explore Tartarus, a mysterious tower that replaces the school.

After a typhoon looms over the school grounds and causes the school's cultural festival's cancellation, S.E.E.S goes to explore Tartarus once more. However, upon hearing the sound of bells ringing, a mysterious phenomenon occurs: the entire party is transported to the Velvet Room, a mystifying place that only their leader can normally visit.

Shortly after, S.E.E.S., along with Elizabeth and Teodor—the residents of the Velvet Room—are suddenly brought to the cultural festival of a certain Yasogami High School. Unable to escape, the team begins to venture around the school in hopes of finding a way back home. Fortunately, they won't have to face this ordeal alone, with another party seemingly being trapped as well...