The all-girls Kikyo Private Academy and Chidori Public High School are polar opposites. With its prestigious history, Kikyo is attended by noble young ladies from distinguished families, while Chidori is infamously full of simple-minded delinquents. It is no surprise that their students clash with their differences. Having a tall stature and fierce appearance, Chidori student Rintarou Tsumugi is often avoided by others despite his gentle heart. One day, while helping out at his family's patisserie, he meets a customer who, after a brief moment, runs away from him. The next day, the customer returns to apologize to Rintarou, introducing herself as the cheerful Kaoruko Waguri. After spending time with Kaoruko, Rintarou appreciates that she does not judge him based on his appearance and looks forward to when they will meet again. However, when Rintarou discovers Kaoruko attends Kikyo, their relationship will challenge the social expectations and dynamics around them.

Despite occasional setbacks, Operation Strix has remained on track to extract sensitive information from the enigmatic politician Donovan Desmond. To this end, spy Loid Forger has managed to maintain his pretend family consisting of his telepathic daughter, Anya; assassin wife, Yor; and their clairvoyant dog, Bond. Still the only one aware of everyone's true identities, Anya tries to sustain the family's cohesion while working to befriend Donovan's son Damian, her Eden Academy classmate. However, Anya's efforts instead earn her another Tonitrus Bolt, bringing her closer to getting expelled and jeopardizing the operation's success. Hearing the news, Loid faints from shock. In his unconsciousness, he reminisces about his tragic past and his journey to becoming a spy. Realizing what Operation Strix means to him and the world, Loid finds renewed motivation. Although they each work toward their own covert goals, the Forgers continue to cherish their chaotic yet blissful family life.

After surviving the entrance exams, Sakuta Azusagawa has finally enrolled in the same university as his girlfriend, Mai Sakurajima. He is gradually getting used to the unfamiliar environment as he attends student gatherings and makes new acquaintances. Everything seems to be going smoothly until Sakuta's friend and Sweet Bullet idol group member Uzuki Hirokawa begins acting out. With fellow Sweet Bullet member Nodoka Toyohama pleading for his help, Sakuta realizes that he has stumbled upon another case of the inexplicable Puberty Syndrome—Uzuki is feeling pressured by the sudden surge of popularity and rumors of a potential solo career. While Sakuta searches for a solution, another occurrence of Puberty Syndrome gradually emerges from the shadows.