A girl named Kazumi wakes up to find that she has been kidnapped and stripped of her memories. She is rescued by two girls claiming to be her best friends, Umika Misaki and Kaoru Maki, who take her back to where they live. While getting settled into this unfamiliar place, Kazumi is attacked by a witch and suddenly transforms into a magical girl!

After discovering her powers, her two roommates reveal to Kazumi that they are magical girls as well, the three of them belonging to a group called the Pleiades Saints whose goal is to fight witches. As Kazumi's "new" life begins, things start to get even stranger when bizarre events start to take place around the city.

Mahou Shoujo Kazumi★Magica: The Innocent Malice explores Kazumi's readjustment to a world she has forgotten and the realization that her true enemies are a lot closer to her than she thinks...