Natsuki confesses to Mitsuru that she and her friends had locked Fuuka inside the school's gymnasium. Yukari, Junpei and Makoto go looking for answers from the delinquents behind Port Island Station and learn from Shinjiro Aragaki that the girls had been bullying Fuuka before the latter disappeared that same night. However as the train nears an inevitable collision, Makoto defeats the Priestess with Junpei before stopping the runaway train. Junpei charges ahead and encounters the Priestess Arcana which overwhelms him. However the trio are ambushed by the Shadows just as the train begins accelerating.
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On another full moon, Mitsuru detects an abnormally large Shadow presence aboard a train and deploys Makoto, Yukari and Junpei to investigate. Makoto also befriends Fuuka Yamagishi and learns of her strained relationship with class bully, Natsuki Moriyama. Not long after as Junpei also joins SEES, Akihiko deduces that they have enough members to begin exploring their school's Dark Hour form, a Shadow-infested labyrinth called Tartarus, where they hope to unearth the mystery of the Dark Hour. Ikutsuki, Akihiko and Mitsuru recruit Makoto to the Specialized Extracurricular Execution Squad-SEES to help them fight the Shadow creatures responsible for the Apathy Syndrome by preying on humans during the Dark Hour midnight phenomenon. After having been unconscious for over a week, Makoto awakens in the hospital to find Yukari, who explains their similarity in having both lost parents during the accident in the past. However they are cornered by a giant creature Makoto awakens to the power of two Personas to defeat the foes. Yukari grabs Makoto and flees to the roof. During the midnight phenomenon, Akihiko Sanada rushes back to the dorm just as it comes under the attack of a swarm of monstrous creatures. Meanwhile Makoto finds himself in a place called the "Velvet Room" and becomes acquainted with Igor and Elizabeth. Afterwards the school's Chairman of the board, Shuji Ikutsuki, asks Yukari to investigate Makoto due to his uncanny characteristics which hint at his "potential" and coincidental circumstances involving the death of his parents during an accident in the city some ten years previous.
The next day, Makoto enrolls at Gekkoukan High School as a sophomore with Yukari and fellow classmate Junpei Iori. Makoto makes his way to the Iwatodai Dormitory where a mysterious boy greets him with a contract after which he meets fellow dorm mates, Yukari Takeba and Mitsuru Kirijo. High school student Makoto Yuki arrives sees a strange phenomenon grips a city-shutting down all forms of technology and causing humans to become encased in coffins.The synopsis below may give away important plot points.