Shin feels dejected over his relationship with Ryo since he returned, but he rejoices over the invitation from Eiko Nikaido, whom he admired since childhood, to a drive, even if it is strictly business.
Like the others with Apathy Syndrome, Shin sits by the shore, thinking of the peaceful memories with his family. Meanwhile, the artificial organic body created to replace Ayane, who is lost wandering in the Sea of Psyche, is on its way to Toyama Bay.
One winter afternoon 10 years ago, simultaneous accidents and natural disasters suddenly broke out in the bay area of Ayanagi City, and many people were infected with Apathy Syndrome and the entire city ground to a halt.
Jun's body, now possessing only Yuki's psyche, is kidnapped by the Marebito in an attempt to stabilize their Personas. Knowing there were risks after discovering her true self, Kanaru still tried to protect Jun.
Jun meets a red-haired girl, Ayane, reading "A Whale's Feather" at the park near his house, and Shin soon realizes the girl is the same as the one always appearing and disappearing with the white feathers.
Takuro and Megumi are skeptical of Sanada, who failed to prevent casualties and was using Shadow Extraction to find the Latents, just like the Marebito. The two were also forming mixed feelings, even doubt, towards their Personas.
Shin and his friends are asked to form a Persona fighting force to combat the Marebito, as well as their leader Kujo. It is up to Shin and his Persona to stop the distortion and bring an end to the Marebito and their twisted goals of exploiting Personas.
Megumi learns about a secret club at the academy called the "Shadow Extraction Circle." Along with Shin and Takuro, he enters the room where the club gathers, and they are surprised to find that the leader of the club is Kanaru.
Shin gets drawn into an incident while he is with his friends. When Ryo learns of Shin's ivolvement, he angrily orders Shin to leave the city. Ryo's cold attitude troubles Shin, who is worried about the ten-year gap in which the brothers grew apart.
Shin transfers to Naginomori Academy and becomes acquainted with his classmates Takuro Sakakiba, Megumi Kayano, and Kanaru Morimoto. A ritual called Shadow Extraction is becoming popular among the kids both at school and in the city.