Makoto returns to Iwatodai ten years after his parents died in an accident. He's introduced as a transfer student who has moved into the Iwatodai Dormitory, but he arrives late because someone jumped in front of the subway, committing suicide. When he arrives at the dormitory, a mysterious boy named Pharos introduces himself and asks him to sign a contract stating that Makoto will accept responsibility for his actions.

The first month at Iwatodai. Welcome to S.E.E.S.! Makoto meets Yukari, Junpei, Mitsuru, Akihiko, Shuji Ikutsuki, and many other classmates at Gekkoukan High School, as well as joining S.E.E.S. and discovering the power of Personas and the dark hour.