Yagami-kun's Family Affairs follows Yūji Yagami, a high school student with a problem: his mother, Nomi, looks very young and Yūji has a crush on her. To complicate matters, his high school homeroom teacher is also infatuated with her due to how young she looks. Nomi is oblivious to all of this and is head over heels in love with her husband, Yōji, and frequently displays this affection very publicly, which causes more embarrassment for Yūji.