In the spring, male student Makoto Yuki transfers to Gekkoukan High School. However, as he heads to his new dormitory, listening to the music on his headphones, he is stopped. More precisely, time has stopped, and the people who were around him turn into coffins. Makoto learns that this period of time hidden between the minute of midnight is called the Dark Hour, a time when monsters called Shadows appear. Suddenly made the leader of his fellow classmates Yukari and Junpei by his upperclassmen Mitsuru and Akihiko, Makoto must learn empathy, his connection to his comrades, and the meaning of death. With the power of his Evoker aimed at his head, Makoto fights against the Shadows threatening to attack his world from the mysterious tower of Tartarus.
In the spring, student Makoto Yuki moves to Iwatodai City, and learns of a hidden period called the Dark Hour, a time when monsters called Shadows appear. After awakening to an ability called Persona, Makoto finds himself intertwined in the battle against the Shadows with his new schoolmates.
- 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. 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. The next day, Makoto enrolls at Gekkoukan High School as a sophomore with Yukari and fellow classmate Junpei Iori. 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. Meanwhile Makoto finds himself in a place called the "Velvet Room" and becomes acquainted with Igor and Elizabeth. During the midnight phenomenon, Akihiko Sanada rushes back to the dorm just as it comes under the attack of a swarm of monstrous creatures. Yukari grabs Makoto and flees to the roof. However they are cornered by a giant creature Makoto awakens to the power of two Personas to defeat the foes.
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. 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. 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. Makoto also befriends Fuuka Yamagishi and learns of her strained relationship with class bully, Natsuki Moriyama.
On another full moon, Mitsuru detects an abnormally large Shadow presence aboard a train and deploys Makoto, Yukari and Junpei to investigate. However the trio are ambushed by the Shadows just as the train begins accelerating. Junpei charges ahead and encounters the Priestess Arcana which overwhelms him. However as the train nears an inevitable collision, Makoto defeats the Priestess with Junpei before stopping the runaway train.
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. Natsuki confesses to Mitsuru that she and her friends had locked Fuuka inside the school's gymnasium. However when her friends went to check on Fuuka that same night, she had mysteriously vanished while the latter developed the Apathy cases after being preyed on by Shadows. That night the SEES members deduce that Fuuka may be trapped inside the Tartarus tower and plan to rescue her. Mitsuru elects him to protect Natsuki at the dorm where he listens to Natsuki's reasoning for bullying Fuuka and relates that Fuuka genuinely considers her as a friend.
Afterwards the SEES members break into the school and indeed find Fuuka inside Tartarus when the Dark Hour strikes. Mitsuru and Yukari come under attack by the Emperor and Empress Arcanas at Tartarus' entrance. Junpei, Akihiko and Fuuka rush to their aid however the Arcanas easily overwhelm all of their Personas. In the midst of the battle, Fuuka also awakens a Persona, Lucia, to defend an entranced Natsuki. With everyone approaching their physical limits, Fuuka uses Lucia to sense the Arcanas' weaknesses and coordinates the SEES members in a collaborative effort which results in the Shadows' defeat. A few days later, Fuuka moves into the Iwatodai dorm and repairs her relations with Natsuki, while life returns to a level of normalcy.
In a post-credits scene, the mysterious boy appears to Makoto and introduces himself as Pharos. Meanwhile at an undisclosed location, a girl awakens from a slumber.