At the stroke of midnight, the Dark Hour appears—a secret hour which most are unaware of. Those not trapped in coffins during this time, unfortunate enough to find themselves conscious, are met by dangerous creatures known as Shadows. A select few, however, possess the potential to wield Persona: a special power used to defeat these beings. This secret group is called SEES (Specialized Extracurricular Execution Squad), and their mission is to uncover the reason behind the Dark Hour's appearance. Only a short while after transfer student Makoto Yuuki begins his residency at Iwatodai Dorm, his Persona awakens after an attack by a strong Shadow. Now recruited into the ranks of SEES, he begins fighting alongside his comrades, as only they can protect humanity from Shadows and prevent the anomaly that is the Dark Hour.

As the season changes from spring to summer, Makoto Yuuki remains alongside the Specialized Extracurricular Execution Squad (SEES). The team continues to defeat Shadows large and small, but they now clash with a new enemy: Strega, a group of rogue Persona users who wish to keep the Dark Hour to their advantage—it seems that Strega may hold a clue to the Dark Hour's true nature. While SEES enjoys summer vacation in Yakushima, they are joined by Aegis, an amnesiac android designed to destroy Shadows. While she proves herself to be a powerful ally, she is inexplicably drawn to Makoto and constantly remains at his side. As they delve deeper into the mysteries of the Dark Hour, the nature of the mysterious connection that binds these two together is slowly unveiled.

As the fall season nears its end, Chidori Yoshino, a member of Strega, abducts Junpei Iori. Meanwhile, Makoto Yuuki and the Specialized Extracurricular Execution Squad (SEES) annihilate the Arcana Hanged Man. Soon after, a mysterious playboy named Ryouji Mochizuki transfers into Gekkoukan High School's Class 2-F. Supposedly having achieved their goal, the members of SEES believe they are free from the battle that has ruthlessly stolen away the lives of their loved ones. And yet, Tartarus and the Dark Hour continue to exist, undeterred by the extermination of the twelfth Shadow. Distraught by their apparent failure, SEES must cope with their personal struggles and discover whose sake they fight for. As Makoto and Junpei's journeys of self-discovery progress, Ryouji's identity and the reason behind Aegis's hate for him become clear.

"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... (Source: ANN)