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.

Kiri Haimura has an obsession with beautiful hair—specifically, cutting it. This bizarre trait is what leads him to seek out a rumored long-haired ghost who lives in an abandoned house on a hill. However, he finds not a ghost, but a beautiful girl with long flowing hair named Iwai Mushanokouji, the Hair Queen, whose hair cannot be cut due to a family curse. Iwai explains that there is a death game surrounding her, and that if she is killed by a cursed object, aptly named a Killing Good, the wielder gets their wish granted. After protecting Iwai from Authors—Killing Goods users—he learns there is in fact a Killing Good passed down in his own family: a pair of scissors used by his ancestor to commit murders. Naming the scissors The Severing Crime Edge, he finds that he is able to cut Iwai's cursed hair with them, setting her free to live a normal life. However, many Authors seek to kill the Hair Queen, and Kiri will have to protect her in this lethal game of fate.

Kazuya, a mild-mannered high school sophomore coming to the end of a very average summer break, receives a digital single lens reflex camera as a gift. His nerdy fascination with its design soon turns to wonder when he realizes this little gadget could really give his social life a shot in the arm! (Source: TBS)

Natsume Tomoharu is a normal high-school student in every way with one exception: he's being followed by the ghost of his best friend, Misao. After moving into his brother's old house, Tomoharu expects to continue living his normal life but is one day left with a mysterious and locked briefcase without any instruction. At first he plans to leave it in storage; however, his house is soon invaded by multiple groups of people after the briefcase. Although still not knowing the purpose of the briefcase, Tomoharu and Misao attempt to escape with it. From there on, Tomoharu tries to learn the secrets behind the briefcase, the connections between it and Misao, and why it has the power to change the world.