Villain or hero, Taira no Kiyomori changed Japanese history forever 900 years ago. Without ever knowing his real father, Kiyomori was raised as a samurai. Together with his stepfather, he wiped out piracy along Japan's western coast, becoming a full-fledged warrior samurai. In an age when samurai were looked down on as members of the lower class, Kiyomori was skillful at winning the hearts and minds of the people. By rounding up surrendered pirates and achieving other successes, Kiyomori eventually became the de facto ruler of Japan.

As a former gang member, Hazama Ichiban witnessed the worst side of the emergency medical system and vowed to become a doctor to change it. With the aggressive passion he learned on the streets, Ichiban has worked his way to becoming a no-nonsense emergency medicine resident. But it is this same passion that he must learn to control when confronted with a situation beyond his help.

Commander Sugata discovered the existence of the Royal Underground Empire Tube, a malignant force that desires to dominate the land, which is based underneath Japan. He recruits five young people, each one specializing in a style of martial arts, and teaches them in the ways of the mystical "Aura Power" energy. A year after he recruited and trained the Maskmen, Tube is ready to strike.

Kazama Yui, a country girl from Kyushu who was recruited by the Dark Director and given the role of the third Saki Asamiya. In the story, Yui was sent to Tokyo to meet up with her long lost sisters, Yuka and Yuma, and they inherited the family's ninja art in order to solve the menace of a psychic terrorist known as the Emperor. Now turned into a trio of kunoichi, they would battle the villain and his army, helped by their mentor Kazuya Yoda and the agents Reia Kido and Obiwan Osho. Yui herself rarely used the Saki Asamiya moniker and showed a very different personality compared to Saki and Yoko, and the series was more focused in fantasy than serious urban crime drama. NOTE: although it has 3 in the title and is loosely related to the other two Sukeban Deka shows this should not be treated as a direct continuation but rather as a standalone show.