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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.

It has been six months since Yoshiki Tsujinaka's best friend, Hikaru Indou, went missing in the mountains and returned a week later with no recollection of what had transpired. Certain that it is not the Hikaru he knows who came back, Yoshiki finally asks Hikaru about it. Suddenly, "Hikaru" reveals his true monstrous form and begs Yoshiki to keep it a secret, as he does not want to kill him. Despite his paranormal nature, "Hikaru" seems almost innocent, full of childlike wonder and eager to experience the summer heat, the countryside, and all kinds of other things in a human body for the first time. And for Yoshiki, it matters little if "Hikaru" is a fake relying on stolen memories—as long as he never leaves again. As Yoshiki desperately clings to "Hikaru" in his intense grief, it becomes increasingly clear that something dangerous and supernatural may have descended from the mountains into their village.

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.

Kitada Gaku, a young man who once aspired to uncover the world's truths through mathematics, finds himself at a crossroads after failing to achieve his dream of competing in the Math Olympiad. With his scholarship revoked, he spends his days working at a school cafeteria, struggling with a sense of aimlessness. Everything changes when he meets a brilliant chef who introduces him to the fascinating intersection of mathematics and cooking. As Gaku embarks on this unexpected journey, he is drawn into a culinary world that's as complex and precise as mathematics itself. A unique and inspiring story where numbers and flavors blend to reveal the beauty of discovery, Mathematics Meets Cuisine opens the door to a new world of gourmet adventure.