Illyaviel von Einzbern is an ordinary middle school student who becomes a magical girl when the magical Kaleidostick Ruby deems her a more suitable master than the sorceress, Rin Tosaka. Rin, who had been tasked by the wizard Zelretch to collect the seven Class Cards containing the spirits of Heroic Spirits from legend, finds that she is unable to change Ruby's mind and must supervise Illya in completing the task of collecting the Class Cards. During Illya's adventures, she receives a friend and rival in a girl named Miyu, the contracted master of the Kaleidostick Sapphire, which similarly abandoned its original master and Rin's rival, Luvia Edelfelt.

After a series of battles, Illya and Miyu were able to collect all Cards and became good friends, while Rin and Luvia remained in Japan by the order of Zelretch. However, the appearance of Kuroe, a girl with a striking resemblance to Illya, soon complicates their lives as she attempts to eliminate Illya.