Takumi Tsuzuki is a student at the exclusive Umenomori Private Academy, where he attends without cost thanks to his childhood friend, Fumino Serizawa. Their relationship, however, is complicated by Fumino's habit of saying the opposite of what she truly feels. School life is further complicated by Chise Umenomori and her outlandish hobbies. After school, Takumi works at his adoptive older sister Otome Tsuzuki's bakery, "Stray Cats," before returning home to sleep. It's a predictable routine. But in Mayoi Neko Overrun, Takumi's daily life takes a surprising turn. Otome is absent, busy helping someone in need. Fumino rouses Takumi from sleep, and he catches a glimpse of her panties. Otome later returns home with a peculiar girl named Nozomi Kiriya, who behaves and looks like a cat. Otome welcomes the runaway into the household, and Takumi's mundane existence becomes anything but as he begins to unravel the mysterious Nozomi's secrets and past.