Three years after her resignation from Kurogin Academy, Yankumi returns as the new homeroom teacher of Akadou Academy's 3-D! Upon her arrival, she discovers that the class is full of delinquents, and is divided into two opposing groups that are always at each other's throats. One of the students, Kazama Ren, is suspected to be behind a series of muggings, and while the rest of the class doesn’t seem to care about his predicament, Yankumi resolves to prove Kazama's innocence.

Determined to teach class 3-D the true meaning of comradeship, Yankumi seeks out different ways to relate and get closer to the students, yet all her efforts seem to be thwarted. Meanwhile, the two heads of said groups, Ogata Yamato and Kazama Ren, decide to have a one-on-one fight to finally determine who's the better boss, but when this turns out futile, they find themselves settling their differences in the most unusual of means.

The Spring Inter-Class Competition is nearing, and now that Ogata's and Kazama's sides have already made peace, Yankumi is more fired-up to have the whole class join and conquer the rugby match. Ichimura "Ichi" Rikiya, Yankumi's student, meets an old classmate from junior high, Takasugi, who seems to be a quiet, studious boy, but actually has a dangerous side to him.

Yankumi, the teachers and class 3-D meet Kaoruko, Kazama's older sister. She visits Akadou Academy, and chastises Kazama upon finding out that he has a part-time job, which is prohibited in school. Amidst the "Springtime Eliminate Delinquency Campaign" organized by Sawatari, Kazama faces the possibility of expulsion for deliberately hitting a police officer, causing him to have a falling out with his sister.

Yankumi talks to her students’ parents about their future during PTC, one of them being Honjo Kengo's dad, a tofu store owner. When he collapses from over-fatigue, class 3-D fears that Honjo will have to drop out, so they decide to raise money to help him out by trying out different jobs. Honjo, on the other hand, encounters an old senpai of his, Narita, who lends him the money he needs – but with serious consequences.

Class 3-D is planning a hook-up party with some girls from the neighboring schools, but Kuraki "Kura" Satoru is indifferent... for he is actually in love with Saki, a sickly girl he met a week prior. Wanting to take a break from the confines of the hospital, she calls Kuraki, and the two go out to have fun, until Saki's disease kicks in. This enrages her parents, and they file a complaint to Sawatari, prohibiting Kuraki from ever seeing Saki again. Unable to bear her student's misery, Yankumi steps in to help.

It's time for Akadou Academy's annual festival, and Yankumi encourages class 3-D to participate. At first, everyone is uncaring, but the promise of girls visiting the school during the event ignites their enthusiasm, and they agree to form a coffee shop named "Hottie Café". Trouble arises, however, when Ogata, Kazama and the others unwittingly piss off Goda Ryuuji, an Akadou alumnus with a notorious reputation, who retaliates by vandalizing the school the night before the festival.

Ami, Kuma's wife, is approaching her due date. While an excited Yankumi prepares for the baby's birth, one of her students, Kamiya Shunsuke, finds himself frustrated when he gets beaten up by an Ara High bully in front of his girlfriend. Subsequent events with his mother and Kuma take a toll on his temper, and Yankumi races to rescue Kamiya when he picks another fight with a bunch of punks, as well as teach him an important lesson about strength.

Class 3-D is awarded for catching a thief during a secret night visit to school, yet their celebration is short-lived when they get into a scuffle with a few classmates who gets themselves involved with a bad crowd. With only a few months left before graduation, Yankumi strives to reunite everyone and restore 3-D's friendship.

It's almost time for the finals, and class 3-D is determined not to fail in order to have a great summer break. Apart from that, they also have to avoid expulsion by not getting into any more trouble, but that appears unlikely when Goda is on the loose again. Swearing vengeance, he raids Akadou Academy and gravely injures Kazama, leading to immense chaos that seems impossible to stop, even for Yankumi herself.