The five girls plus Coco, Nuts, and Milk all go to visit a castle-themed theme park, where they dress up as princes and princesses and go off to have a fun-filled day. However, Coco and Nuts end up kidnapped! The girls have to save them with the help of two inhabitants of the Mirror Country, Hidarin and Migirin, by battling Shadow, an evil clown, and five girls who are also from the Mirror Country that look very familiar...

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. [Written by MAL Rewrite]

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. [Written by MAL Rewrite]

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. [Written by MAL Rewrite]