After the events of the TV series, the 18 year old Yoko Godai has abandoned her special agent Saki Asamiya name to return to her normal life, and is now studying for college entrance exams. However, she accidentally bumps into a young man named Kazuo Hagiwara trying to escape from a group of hitmen, and learns that he comes from Sanko Academy, a private school located in a remote island known as Hell's Castle. The school is ruled by a former revolutionary thought to be dead named Hattori who is trying to brainwash students into terrorists to help him stage a fascist coup d'etat in Japan.

After the events of the previous film, the 17 years-old Sukeban Deka III, Yui Kazama, works for the Juvenile Security Bureau along with her older sisters Yuka and Yuma. This organization is led by politician Kuraudo Sekin, who fights juvenile crime in heavy-handed manners, to the extent to equip his student agents with triple-bladed yo-yo weapons. However, when Sekin's methods become too zealous, Yui quits the bureau and refuses to undertake undercover missions for them. It is soon discovered that Sekin's actual goal is to overthrow the Japanese government, and the Kazama sisters, along with a gang of young outcasts, have to stop him.