"Cinderella Nine" centers around Tsubasa Arihara, a high school student with a passion for baseball. After transferring to Shinonome Academy, Tsubasa discovers that the school lacks a baseball team. Determined to change this, she sets out to form a girls' baseball team, despite the initial lack of interest and support from her peers. The narrative follows her efforts to recruit members, train the team, and compete in tournaments, highlighting the challenges and triumphs of building a team from scratch.

The main characters include Tsubasa, the determined and optimistic protagonist; Riko Tsukishima, a skilled but reserved pitcher; and Yuki Tachibana, a former track athlete who joins the team. Other key members include Nozomi Kiyosawa, a cheerful and energetic player, and Ayaka Saitou, a disciplined and serious team captain. Each character brings unique skills and personalities to the team, contributing to its growth and dynamics.

The plot progresses through the team's development, from their initial struggles with coordination and teamwork to their eventual participation in competitive matches. The series emphasizes themes of perseverance, friendship, and the pursuit of dreams, as the characters overcome personal and collective obstacles. The narrative balances moments of intense sports action with character-driven subplots, exploring the individual motivations and backstories of the team members.

As the story unfolds, the team faces various challenges, including rival teams, internal conflicts, and the pressure of competition. The series portrays their journey with a focus on the camaraderie and determination required to succeed in sports. Through their experiences, the characters grow both as athletes and individuals, culminating in their efforts to achieve their shared goal of becoming a formidable baseball team.