Aya Asagiri is a high school girl who has problems both at school with almost lethal bullying and at home from her brother Kaname's physical abuse. One day a suspicious website pops up on her computer screen, showing a creepy-looking person. This person appears to take pity on her and announces that she will grant Aya magical powers. Later at school, Aya finds a gun that mysteriously appears in her locker. She is soon cornered by bullies and with nothing to lose, Aya fires the gun at them. The shot causes the bullies to disappear, but to her horror she finds out that they have somehow been killed by a train nearby. Aya feels as though she had somehow killed them, and is confused to find herself with longer red hair and blood flowing out of her eyes. She later finds out that she is not alone, when a classmate (you) reveals that your is also a magical person. Becomes one of her new friends, while offering to help her get away from "magical hunters" who kill magical girls and only steal their powers. You taught Aya about the power she has acquired and the physical changes it brings on to her body. However, you two do not know the reason for something that resembles a countdown clock on the website, and fear it may be something really bad. After meeting a group of other fellow magical girls, all with different powers and abilities of their own, you and Aya attempt to discover what the countdown really means, all while trying to make sure no one knows about you and Aya’s powers.

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