Nogizaka Haruka no Himitsu centers around Yuto Ayase and Haruka Nogizaka. Yuto is seemingly ordinary, but Haruka is attractive, intelligent, and rich, which prompts other students to idolize her and even give her French nicknames like "Nuit Etoile" (The Silver Star of the Night) and "Lumiere du Clavier" (The Shining Princess on the Piano). One day, Yuto wanders into the school library in order to return a book and accidentally stumbles upon Haruka's deepest, darkest secret: she is a diehard fan of anime and manga (an otaku). Promising Haruka to keep this a secret, Yuto becomes her advisor and confidante, earning some viciously envious glares from his fellow schoolmates.