Elite Yankee Saburou is set in Tokumaru Academy, a private high school known for its delinquents. In particular, two former students, the brothers Ichirou and Jirou Ookouchi, became legends throughout the prefecture for their fierceness. Naturally, when the third Ookouchi brother Saburou entered the school, everyone feared for the worst. However, Saburou happens to be an ordinary high school student. He's typically shy and is a bit of an otaku. But through misunderstandings and bad luck, he begins to develop a reputation as an "elite yankee."

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