Outwardly, SEES—the Specialized Extracurricular Execution Squad—appears to be an entirely ordinary club at Gekkoukan High School. In truth, however, it is a group of students who investigate a phenomenon called the "Dark Hour" and eliminate entities known as "Shadows." Only chosen individuals with "potential" can recall the occurrence of the Dark Hour, while others will "transmogrify" into coffins and become vulnerable to Apathy Syndrome—a condition that places its victims in a trance-like state and causes them to lose their will to live. Transfer student Minato Arisato is one such individual capable of remembering events that take place during the Dark Hour, despite being unaware of his ability. Upon arriving at the school, he encounters a mysterious figure who asks him to sign a contract stating he will take responsibility for his own actions. Shortly after, he is confronted by the members of SEES, who place him under secret surveillance because they believe he possesses a potential far greater than that of any other member. One night, Minato is suddenly awakened by Yukari Takeba when a Shadow attacks their dormitory during the Dark Hour. Feeling compelled to fight the Shadow, he grabs Yukari's gun but, instead of firing at the Shadow, he turns it on himself, thereby awakening his "Persona." Armed with his new powers, Minato joins SEES to uncover the mystery behind the enigmatic phenomenon.