Makoto Yuki - Minato Arisato is an orphaned teenager who transfers to Gekkoukan High School at Tatsumi Port Island and much to his confusion, finds himself experiencing strange phenomenon on his way to the dorm. Arriving at the Minatodai Dormitory, Makoto is greeted by a boy named Pharos and signed a contract the boy has prepared, before confronted by Yukari Takeba and Mitsuru Kirijo. The next day, on his first day in Gekkoukan High School, he befriends one of his classmates, Junpei Iori. The following night, Makoto dreams about a mysterious man named Igor with his assistant, Elizabeth, in a room called Velvet Room who are telling him of the journey he will face. Meanwhile, Mitsuru, Yukari, and the chairman of the school, Shuji Ikutsuki, observing Makoto from the command room, the Minatodai Dormitory comes under the attack of terrifying creatures called Shadow, injuring one of their team members, Akihiko Sanada. While Mitsuru and Akihiko fend off the Shadows downstairs, Yukari and Makoto are cornered by a gigantic one once they arrived there. In the nick of time, Makoto awakens to the power of his Persona, Orpheus, that then turns into Thanatos, easily defeating the Shadow. After recovering, Makoto finds out there exists a hidden period of time between one day and the next known as the Dark Hour. During this phenomenon time itself seems to come to a halt and unbeknownst to humanity, their bodies become transmogrified into coffins while Shadows roam freely. Only those who have awakened the power of Persona can experience the Dark Hour and stand any chance of stopping the Shadows. They invite him to join a covert club at Gekkoukan High called the Specialized Extracurricular Execution Squad — S.E.E.S., whose members have but one goal: to rid the world of the Shadows, which Makoto immediately accepts simply because he was asked to. Not long afterwards, Akihiko also recruits Junpei into their team and brings them to their school that turns into Shadow's nest during Dar
After realizing the value of life and the importance of his own allies, Makoto finally got his smile back. As spring turns into summer, he finds himself learning more about those comrades and getting closer to them. He even meets new friends, including Aegis, an anti-Shadow android, Ken, a grade-schooler who seeks to get revenge for his late mother, and Koromaru, a dog who can use a Persona. Makoto wishes that everything will continue just as they are. However, little by little, the pieces and people in Makoto's new, happy life begin to fall apart, and he is forced to suffer the loss that comes with it.
The season turns to autumn. The fight of the protagonist and his group S.E.E.S. with the strange monsters called ‘Shadows’ is getting closer to the end. Makoto and his allies engage in life-or-death battles with Shadows in order to end the Dark Hour. Through the battles, some must face the deaths of friends and family, some must notice what precious things must be protected, and some must find meaning in the battles that have occurred. In front of Makoto, the mysterious transfer student Ryouji Mochizuki appears. When the group greets a new morning, the gears of fate begin to turn. A fight revolving around each of the heroes' bonds begins...
"The time of destruction is coming ever closer without a doubt. It cannot be stopped." To know death, to gaze at death, to face death. Makoto and his allies have grown through the many meetings and partings they have experienced. Their fight might not be for the sake of the world, but for themselves. Even so, they have continued to fight, believing that there are peaceful days waiting at the end of the battle. However, a boy says that destruction is the fate that humanity must shoulder. The boy they believed to be their friend tells them the truth of the situation without an emotion on his face. The season changes to winter. Makoto makes a decision in order to greet the spring that is waiting beyond...
High school student Shin Kamigo and his younger brother Jun reunite with their older brother Ryo, a member of the Ayashiro City Police Department, for the first time in 10 years. At that time, a series of strange incidents occur in Ayashiro City, such as the sudden disappearance of a submarine crew while on the submarine, a spiritless demonstration that turns the world upside down 10 years later, and a case of an overturned corpse. . The student showed a cruel appearance. Shin, who tracks down the organization behind a series of incidents and gets involved in them, awakens the "persona" in him.
The strange deaths continue, with the most recent victim discovered hanging from a telephone pole. Yu, Chie, and Yosuke begin piecing things together and determine that these grisly murders are connected to that other world inside the TV. Yu and Yosuke decide to go back in, much to Chie's disapporval. Once more will the two boys venture into the unknown, with rope at waist, and fear in Yosuke's heart.
When Yukiko appears on the Midnight Channel, her best friend Chie leads the charge to rescue her. However, the police are out in force and arresting any suspicious characters - including Yu and Yosuke. When Chie goes to the station after them, she reports Yukiko as missing. But the police seem to suspect her involvement in the death of the TV hostess.
Yu faces off against Margaret, after falling into an illusion of him and his friends having a celebration to mark their leader's last day in Inaba. An ancient goddess reveals to Yu how he obtained the Wild Card and the ability to enter the TV. Yu's last day in Inaba may be his last day period, unless he can accept the truth.