Across the world, heinous creatures known as phantoms drain the life force of their human victims, and the only ones capable of defeating them are magical girls. But one being challenges this conflict between good and evil: the shadow phantom Shade, who has protected the 16-year-old Tanpopo Ohanami from other phantoms and her occasional missteps since her childhood.

One day at school, Tanpopo is called upon by the special anti-phantom organization Butterfly responsible for managing magical girls. They believe Tanpopo has a great potential to become a powerful magical girl herself, but Shade warns her that should she become one, they will become enemies. All Tanpopo ever wanted was to fight alongside her most trusted friend—but when she inadvertently awakens her powers, she realizes that the truth behind both phantoms and magical girls is a far cry from the reality she once knew.