Cross Ange: Rondo of Angels and Dragons is set in a world where the existence of magic is accepted, and follows the story of Angelise Ikaruga Misurugi, a princess of an empire that oppressed those who are different. After she finds out that she is one of those "different" people, her life changes dramatically as she is cast out from her royal life and sent to Arzenal, an isolated island where those who have been cast away by society live. There she meets other girls who fight against dragons using giant mechs called "Paramail".
Cross Ange focuses on the struggles of Angelise as she comes to terms with her newfound identity and learns to fight alongside her new comrades at Arzenal. Along the way, she discovers secrets about her past and discovers more about the mysterious dragons that threaten humanity's existence. She also must confront prejudices both within herself and from those around her as she strives to protect what is important to her.