Ryō Kanzato, an officer in the Ayanagi Police with the rank of Superintendent, had been dispatched to a Japanese Coast Guard PLH ship after Japanese Coast Guard crewmembers discovered that their Deep Submergence Vehicle had its entire crew missing, baffling some of them. Meanwhile, mysterious deaths had been reported throughout the city once more. Ryō had rescued Yumi Tasaka, who had been under police custody, from being killed by an unknown assailant with his Persona. Ryō's siblings, Shin and Jun, arrive back in Ayanagi City in the course of his investigation and battle against the assailant with his own Persona. After Shin's arrival, his Persona had awakened and killed the same assailant's Persona after it had threatened him earlier during a walk around the city.
The stage is Ayanagi City, a city near the Japan Sea. It is a futuristic city that was built to carry out the recovery from the calamity caused by the "Apathy Syndrome" ten years previous. High school student Shin Kanzato with his little brother Jun, meet with their elder brother Ryou, who is the chief of the Ayanagi City Police, again after ten years. At that time, a series of strange incidents happen in Ayanagi City such as the crew of a submarine that suddenly disappears while in their submarine, or a spiritless symptom which disturbs the world after ten years, or the case of the inside out corpse where a student took on a cruel appearance. Ryou tracks down the organization behind the string of incidents, and having become involved in the incidents, Shin awakens the "Persona."
