Fujimi Orchestra is, at first, primarily about Tonoin and Morimura's romance, but the story follows the lives of Kei and Yuuki, and their musical careers. After Yuuki says he wants to quit the orchestra because of Kei, Kei steals his violin and leads him to his house, where Kei rapes Yuuki. After it is done and Kei is setting out things to eat for Yuuki, he confesses love, and tells him that Kawashima does not love him, which leads to Yuuki running out of the building and falling down a flight of stairs. Kei is completely mortified, and concerned while Yuuki is recovering. In the end, Yuuki decides to stay with Fujimi Orchestra, and Kei "tries" to stop his urges on him, but when Yuuki loses focus, he takes him in the back room where he makes several passes to him.