A 16-year-old girl named Yoko Godai emerges from a childhood spent confined behind iron masks, her past shrouded in mystery. A police agent named Nishiwaki, a former colleague of the original Sukeban Deka's handler, frees her and offers her a chance to earn her freedom by joining the undercover Sukeban Deka program. In exchange for his help in locating her missing father, Yoko accepts, taking on the name and identity of the presumed-dead original Saki Asamiya and wielding a modified steel yo-yo as her signature weapon.

Unlike her predecessor who worked largely alone, this new Saki Asamiya is joined by two loyal sidekicks. Yukino Yajima is a refined heiress from Kyoto and a martial arts expert, while Kyoko Nakamura, nicknamed Marble Okyo, is a street-smart fighter from Osaka who uses marbles as projectile weapons. Together, this trio battles a wide range of criminal organizations and corrupt authority figures infiltrating Japan's high schools.

The central narrative arc of the series revolves around a powerful syndicate called the Seiroukai and its enigmatic leader known as Soto, a man connected to Yoko's past. Soto, who returns from the United States after adjustments to his pacemaker, plans to use the Seiroukai to take over Japan. In a key confrontation, Saki infiltrates the Seiroukai by stealing the identity of a candidate member named Ijuin Kaname. Her disguise is eventually discovered, leading to a tense confrontation with Soto in an underground pathway. During their fight, both realize they are playing the same melody on their music boxes, hinting at a deep, unresolved personal connection between them as Saki desperately demands to know his identity and his intentions toward her. This recurring mystery of Soto's true nature and his link to Yoko's childhood forms the emotional and dramatic core of the season.

Throughout its 42-episode run, the series maintained the franchise's signature blend of juvenile delinquency, action, and police procedural drama while surpassing the first season in popularity. Production was physically demanding for lead actress Yoko Minamino, who faced grueling shooting schedules and often went to school with fake blood and glue still on her body from filming. The character's iconic iron mask, worn in early scenes, was a particular point of dislike for the actress. The series concludes with the resolution of the Seiroukai arc before leading directly into the 1987 theatrical film Sukeban Deka The Movie, which follows an 18-year-old Yoko Godai as she is pulled out of her quiet life studying for college exams to face a new threat.