After the events of the Sukeban Deka II TV series, the now 18-year-old Yoko Godai has abandoned her special agent Saki Asamiya name to return to her normal life and is studying for college entrance exams.

However, she accidentally bumps into a young man named Kazuo Hagiwara escaping from a group of hitmen, and learns that he comes from Sankou Academy, a private school located in a remote island known as Hell's Castle.

They are contacted by Yoko's former caretaker Nishiwaki, who reveals Hattori is actually a former revolutionary leader, Jishu Kita, thought to be dead after the Dark Inspector defeated him five years before.

The team fights their way through Gakuan Academy and its elite juvenile fighters, and Megumi sacrifices her life to save Saki from a lethal dart thrown by Hattori, making up for her betrayal.

While the rest of her team prepares to blow up the island, Asamiya fights Hattori again, but this time the Sukeban Deka defeats him with her new yo-yo, almost crushing her own arm in the process, and kills him with electricity.