Sasami Iwakura has been endowed with magical powers since birth; but at age three, she is forbidden by her parents to use them. So she decides to keep her magical powers a secret. But at the start of a new term, she encounters the new transfer teacher Washu and her pet Ryo-Ohki, and her life is about to change.

The first series/season is dedicated to character development as we are introduced to magic girls Sasami, Misao, Makoto, Tsukasa, and An-an. As the girls discover their awakening powers, they also learn a bit about themselves as they train with Washu and Daimon as part of their "cooking club." This culminates in their taking a trip to the magic world, where they compete against other magic squad teams, some having boys in them.

The second series/season is dedicated to plot, where Sasami's magic girl squad's activities have impressed the Chief Sorceress. As such, she wants those girls as part of her plan to change the human world (Earth), which she sees as too corrupt. The girls, especially Misao, must not only learn to master their abilities and magics, but also learn to face their own fears, lack of understanding, and the like as they walk a dark road set down before them by the Chief Sorceress.

This anime also features Misao (Shinohara) and Sasami's homeroom teacher Mihoshi.