The story of Mei no Naisho centers around Mei Haruna, a boy raised as a girl by his witch mother due to his feminine appearance and identity. When his mother passes away, Mei enrolls in an all-girls high school and moves into the dorm with his talking cat familiar, Abel, and his dorm mate, Fuuka Honjou, a member of the school's public morals committee. Despite his efforts to conceal his true gender, Mei is revealed to be male after a magical mishap in the bath with his new friends. Though initially shocked, Mei is allowed to stay at the school with the help of the perverted student council president. The next day, Mei confesses his witch status and male identity to his classmates, who accept him and admire his magic abilities.
