At the center of Kagura ga Yuku! is the student council vice president, Kagura, whose entire world revolves around the student council president, Kanamori, to whom she has devoted herself for over ten years. Her unwavering dedication dictates her every action, with Kanamori's happiness and well-being being her sole priority. This dynamic is thrown into disarray when a female transfer student, Misono, arrives at the school. Kanamori is immediately smitten, experiencing love for the first time. However, he is too timid and hesitant to act on his feelings or even approach Misono.

In response, Kagura takes it upon herself to become the architect of Kanamori's romance. Believing that nothing is impossible when it comes to serving her beloved president, she throws herself into the mission of conveying Kanamori's charm and virtues to Misono, all while navigating the absurd situations that arise from her over-enthusiastic and literal-minded methods.

The setting is a lively school environment, where the comedic tension stems from the contrast between Kagura's hyper-competent, take-charge attitude in all matters concerning Kanamori and her obliviousness to her own feelings. The narrative progresses through a series of escalating comedic schemes orchestrated by Kagura, including a home date at Kanamori's mansion and a chaotic outdoor school trip. The central conflict deepens with the arrival of a new character, a girl named Takao who is introduced as Kanamori's fiancée, creating a potential love rival and forcing Kagura to confront new complications. The story builds toward Kanamori finally confessing his love to Misono, testing the limits of Kagura's loyalty and the trio's relationships in a hectic student council comedy.