In the second season the story continues exactly where it left off previously. Professor Itsuki's Fermentation Cellar and laboratory is ready for operation and with Sawaki Tadayasu's unique gift to see and communicate with microbes to help, Itsuki's motley group of students begin to process different fermented products like soy sauce and sake. (Source: ANN)

One could say that freshman college student Tadayasu Sawaki has a wide range of vision. He has a peculiar ability that allows him to see microorganisms with the naked eye. Sawaki can see all sorts of microbes, from the fungi that cause athlete's foot to the yeast used to make alcohol, with him perceiving his little friends as cute chibi creatures. Attending an agricultural university, his talent piques the interest of numerous professors, including Professor Itsuki, who specializes in fermentation. Sawaki starts school indifferent toward his ability, choosing an agricultural school in Tokyo. However, with the help of the eccentric community around him, he slowly learns to appreciate these visible microbes and his talent. The whimsical cast of professors and classmates attending the university almost makes Sawaki seem normal despite his ability. [Written by MAL Rewrite]

Shizuku Mizutani is apathetic towards her classmates, only caring about her grades. However, her cold view of life begins to change when she meets Haru Yoshida, a violent troublemaker who stopped attending class after getting into a fight early in the school year. He is not much different from her, though—he too understands little about human nature and does not have any friends. Much to Shizuku's surprise, he proclaims that she will be his friend and immediately confesses his feelings towards her upon meeting her. Because of her lack of friends and social interaction, Shizuku has a hard time understanding her relationship with Haru. But slowly, their friendship begins to progress, and she discovers that there is more to Haru than violence. She begins to develop feelings for him, but is unsure what kind of emotions she is experiencing. Together, Shizuku and Haru explore the true nature of their relationship and emotions. [Written by MAL Rewrite]

Rumors tell about an ageless girl who only comes out at night, living in a mansion in the middle of the forest. Some say that she is a living doll with a soul. Upon hearing these rumors, Akari Amano seeks out this girl, only to find herself lost as she treks through the woods amidst the darkness. A vampire named Sophie Twilight saves her, turning out to be the rumored girl. However, unlike the vampires told in myths, Sophie does not attack humans and instead orders her blood online. Akari instantly becomes charmed with her doll-like appearance and proceeds to abruptly move in with her, thus starting their life together. [Written by MAL Rewrite]