Fresh out of college, Kumiko Yamaguchi, a young and idealistic woman, achieves her lifelong dream of becoming a teacher. She is assigned to Shirokin Gakuen, a private all-boys high school, and is given charge of class 3-D, a group of delinquents notorious for driving away their previous homeroom teachers. Led by the cool and intelligent Shin Sawada, the students immediately try to make her quit through various acts of harassment and rebellion. What they do not know is that their seemingly naive new teacher, who wears a tracksuit and keeps her hair in pigtails, is Kumiko Yamaguchi, the fourth-generation heir to the Oedo Group, one of Tokyo's most powerful yakuza clans. Raised by her grandfather, the clan boss, after her parents died, she possesses incredible fighting skills and a deep understanding of loyalty and honor.

Despite her yakuza background, which she must keep a secret to avoid being fired, Kumiko refuses to give up on her students. Her persistence, unorthodox methods, and willingness to fight to protect them gradually earn her their respect. The students, particularly Shin, begin to see her not as an easy target but as a dedicated teacher who cares about their futures. Shin is the first to discover her secret identity. Throughout the school year, Kumiko uses her unique upbringing to help her students navigate various problems, from gang fights with rival schools to personal family issues and troubles with other teachers. She is constantly at odds with the scheming vice-principal, Goro Sawatari, who is always looking for a reason to expel the students of class 3-D and get rid of their troublesome teacher.

The first season focuses on the original class 3-D at Shirokin Gakuen, including memorable students like Shin Sawada, Haruhiko Uchiyama, Youichi Minami, Teruo Kumai, and Takeshi Noda. The season culminates with their graduation, a testament to Kumiko's success where her students, once written off as hopeless, find their own paths.

The story continues in a second season, where Kumiko, now working at the all-boys Kurogin Gakuen, is once again assigned to teach the troublesome class 3-D. While the setting and students are new, the core narrative repeats as she wins over a new group of delinquents, including Hayato Yabuki and Ryu Odagiri, using the same blend of tough love, martial arts, and secret yakuza wisdom. This season also sees the return of former student Teruo Kumai as a gym teacher, who acts as a bridge to the previous series. A third season follows the same successful formula at Akadou Gakuen, where she befriends a new class of misfits, including Yamato Ogata. The live-action story concludes with a theatrical film, Gokusen: The Movie, which brings together students from all three seasons to help Kumiko when she faces her greatest challenge yet, threatening not only her job but her life as she protects a new generation of students. The narrative arc throughout the series follows a consistent pattern of the underdog teacher, armed with an unlikely secret, transforming the lives of troubled youths by believing in them and fighting for them, all while trying to keep her yakuza identity hidden from the faculty and her students.