Nogizaka Haruka no Himitsu centers around Yuuto Ayase and Haruka Nogizaka. Yuuto 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, Yuuto 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, in other words, a regular otaku. Promising Haruka to keep this a secret, Yuuto becomes her advisor and confidente of some sort and hangs out with her more, though earning some viciously envious glares from his fellow schoolmates.