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.

A.D. 2034. It has been two years since Motoko Kusanagi left Section 9. Togusa is now the new leader of the team, that has considerably increased its appointed personnel. The expanded new Section 9 confronts a rash of complicated incidents, and investigations reveal that an ultra-wizard hacker named the Puppeteer is behind the entire series of events. In the midst of all, Batou, who was stalking the case on a separate track, encounters Motoko. She goes away after saying, Stay away from the Solid State Society. Batou is left with a doubt in his mind. Could Motoko be the Puppeteer? The series of intriguing incidents that Section 9 faces gradually link together almost artistically. Who is the Puppeteer? What will happen to Batou's relationship with Motoko? What is the full truth behind this carefully planned perfect crime? And what will the outcome be? Mysteries surround the Solid State Society... (Source: Production I.G.)

In the 11th year of the Meiji Era, the end of the samurai shogunate and the prohibition of swords has left Japan with lasting scars. Displeased by these recent changes, many former samurai plot against the new government, inciting a wave of bloodshed. To counter this movement, the government constructs a colossal prison in the middle of Lake Biwa. Unofficially assigned to help the police arrest criminals, Tenka Kumou also serves as a ferryman to the Lake Biwa prison with the help of his two younger siblings: the ambitious Soramaru and the enthusiastic Chuutarou. Together with the former Fuma ninja Shirasu Kinjou, the Kumou brothers live a frugal and joyful life mostly dedicated to studying and training. However, behind this relatively uneventful daily routine, the specter of the Orochi curse is starting to spread its shadow over the city of Oumi. According to legend, every three hundred years, Orochi reincarnates in a human vessel—and it is believed that this is the harbinger of an imminent catastrophe. As various groups clash in search of Orochi's vessel, some aim to seal the curse, while others have darker plans in motion.

In ancient times, some witches married their familiars, who had taken human form, giving birth to a lineage of ogres. One such ogre is Morihito Otogi, who while appearing completely human, still retains the inhuman strength of his bloodline. Nico Wakatsuki is a young witch and Morihito's childhood friend, but as part of her education, she had to go to the Witches' Holy Land to train and part ways with Morihito. Years later, just before Morihito's first year of high school, Nico returns home with one goal in mind: to claim him as her familiar. While most witches choose a cat or a bat, Nico has her heart set on Morihito in more ways than one. Although seemingly oblivious to her true feelings, Morihito and Nico end up living together under the same roof with both of Morihito's parents elsewhere. While reluctant at first, Morihito accepts his new role, determined to help Nico seamlessly fit back in with human society and protect her from fated disaster.