Tadayasu Sawaki, a first-year student at an agricultural university in Tokyo, possesses a peculiar and powerful gift. As the heir to a family that produces koji mold starter, he can see and communicate with microorganisms and bacteria with his naked eye, perceiving them as adorable, chatty, animated creatures. He enrolls at this unique university alongside his childhood friend Kei Yuki, whose family runs a sake brewery, but soon finds his secret is not entirely safe.

Professor Keizo Itsuki, an eccentric and fermentation-obsessed elder, already knows of Sawaki’s ability through the young man’s grandfather and eagerly recruits him into his laboratory. Assisting Itsuki is the brilliant but volatile postgraduate student Haruka Hasegawa, a wealthy, sharp-tongued woman who initially doubts Sawaki's power but comes to rely on it for their research. The lab becomes a hub for an odd assortment of students, including Hazuki Oikawa, a germophobe who constantly carries disinfectant; Aoi Muto, the beautiful but troubled president of the UFO club; and the scheming sophomores Kaoru Misato and Takuma Kawahama, who try to use Sawaki’s abilities to brew and sell illegal sake on campus.

As the semester progresses, Sawaki uses his ability to help the lab with various fermentation projects and school events, from identifying spoiled ingredients to saving classmates from food poisoning. A major narrative arc unfolds when the lab discovers that Haruka Hasegawa has made a promise to her overbearing father: she will leave the university and enter an arranged marriage. Unwilling to lose her, Professor Itsuki and the entire lab group rally to convince her to stay, leveraging the full, chaotic support of the agricultural university to fight for her freedom. In a climactic decision, Hasegawa must choose between her family's obligations and her passion for the work and people she has come to love at Agri U. The series also adapts a controversial subplot involving a powerful aphrodisyal created by the professor, which leads to surreal and complicated situations among the students during the school festival. Throughout these events, Sawaki also contends with the return of his missing friend Kei, who reappears dressed in gothic lolita clothing and harboring deeper personal feelings for Sawaki, further complicating the group's dynamic.