Wagamama High Spec is a romance visual novel in which the player assumes the role of Kōki Narumi. With multiple plot lines, the player's choices will steer the story to different endings.

The story revolves around Narumi Kouki, a high school student who also draws a manga serialized in a weekly magazine. Because the manga he draws is a risqué romantic comedy, he keeps this fact a secret from everyone around him, with his younger sister Toa and his sister's best friend Mihiro being the only ones who know.

But one day, as the student council president Rokuonji Kaoruko is searching for male members for the student council, she finds out that Kouki is the manga's author. Kouki joins the student council in exchange for Kaoruko not revealing his secret. However, the vice president, Sakuragi R. Ashe, strongly opposes him joining, and in the midst of all this, various requests and troubles of students begin to pile up.