Fresh out of college, Kumiko Yamaguchi’s lifelong dream is to become a high school teacher. She is hired at Shirokin Gakuen, a private all-boys school, but is immediately assigned as the homeroom teacher for class 3-D, the notorious dumping ground for the school’s most hopeless delinquents. The students, led by the cool and observant Shin Sawada, initially try to force her to quit through intimidation and pranks. However, their plan fails against Kumiko’s bizarre persistence, unshakable optimism, and surprising physical aggression.

What no one at the school knows is that Kumiko, nicknamed Yankumi by her students, is the 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 martial arts skills and a deep understanding of the street code of honor, which she inadvertently applies to her teaching methods. She wears a tracksuit, speaks in yakuza slang, and has a habit of running from police officers, but her secret identity must be protected at all costs. If the school board discovers her background, her teaching career will be over.

Throughout the first season, Yankumi uses her unconventional yakuza-honed tactics to protect her students from real-world threats, including rival gangs, loan sharks, and corrupt authority figures. Despite her secret, her core students—including the loyal Shin, hot-headed Youichi Minami, gentle giant Teruo Kumai, blonde-haired Haruhiko Uchiyama, and the playful Takeshi Noda—gradually come to respect her unwavering dedication. They give her the affectionate nickname Yankumi, a blend of yankee (delinquent) and sensei. While Vice-Principal Goro Sawatari constantly schemes to get her fired, Yankumi fights to keep her class from dropping out, teaching them that loyalty and honor matter more than academic scores.

The live-action series spans three seasons and a concluding theatrical film, following a similar narrative pattern each year. In each season, Kumiko transfers to a new all-boys high school (Kurogin Gakuen in season two, Akadou Gakuen in season three) after an incident involving her secret nearly comes to light. At each new school, she is inevitably assigned to teach the most violent and apathetic class of third-year students. Although the supporting cast of students changes each season to feature new young actors, the core dynamic remains the same: Yankumi must earn the trust of a new group of delinquents while hiding her yakuza lineage from the administration and solving their personal crises with her fists and her heart.

Notable narrative arcs include the students discovering her true identity but choosing to keep it secret, Yankumi dismantling a drug ring targeting her students, and the recurring theme of the graduation ceremony, where her toughest students finally acknowledge her as the best teacher they ever had. A television special, Gokusen Special: Sayonara 3-nen D-gumi, served as an epilogue to the first season, and the storyline concludes with the 2009 film Gokusen: The Movie, which brings together cast members from all three seasons for a final confrontation. Throughout the series, Kumiko struggles to balance her two identities: the gentle, idealistic teacher and the powerful, heir-to-the-syndicate fighter, proving that one can be a boss by taking care of people, rather than by ruling them.