A teenage delinquent and gang leader named Saki Asamiya finds herself in prison, with her mother also incarcerated and on death row for the alleged murder of her father. Her life takes an unexpected turn when she is visited by a mysterious government agent, Kurayami Shirei, who works for a shadowy branch of the Cabinet known as the inner cabinet intelligence division. He offers Saki a deal to secure her freedom and commute her mother's death sentence in exchange for becoming an undercover operative in a new Sukeban Deka project. As a Sukeban Deka, or delinquent detective, Saki is given a special weapon and badge, a super-dense metal yo-yo that she wields with deadly precision. Her handler, a police officer named Jin Kyoichiro, assigns her to infiltrate various high schools and neutralize criminal gangs and corruption that regular police cannot touch.

In the feature film continuation of the television series, Saki faces her most dangerous adversary yet in the form of a megalomaniacal high school principal. This villain operates a secluded island institution for delinquent students, which secretly functions as a facility for brainwashing teenagers into becoming obedient soldiers for a shadowy syndicate. To penetrate this heavily fortified stronghold and dismantle the operation, Saki must join forces with two other Sukeban Dekas and her ally known as Marble Girl. Together, they confront the principal and the evil Mizuchi crime family, including the formidable sisters Remi, Ayumi, and Kumi, in a final, violent showdown that tests Saki’s resolve and her skills with the yo-yo.