Shibaki is a high-school boy whose only interest is girls. Except he's been branded as the most perverted boy at school and the girls avoid him like the plague. One day he finds a book in the library about how to summon witches. An apprentice witch named Rurumo appears to grant him a wish. Shibaki helps Rurumo and she in return refuses to take his soul. When the story starts, Shibaki wishes he could see Rurumo again. His wishes is granted immediately as Rurumo falls from the sky and crash lands in front of him. He finds out that as punishment for not taking his soul she's been busted down to an apprentice demon. Now, she must complete the task of getting Shibaki to use up 666 magic tickets that grant wishes before she can become a witch again. However, what she doesn't know is that each time he uses a ticket it shortens his life. When the last ticket is used up, Shibaki will die. Shibaki knows this because Rurumo's familiar black cat Chiro tell him as part of the "contract" for giving him the tickets. Now, Shibaki has a choice, make a wish and help Rurumo become a witch again or resist the temptation and try to save his own life.
After experiencing a bizarre dream, Madoka Kaname, a kind 14-year-old girl, encounters a magical creature named Kyube. Madoka and her friend Sayaka Miki are offered the opportunity of gaining magical powers if they agree to make a contract with the strange little being. He will also grant them one wish, but in exchange they shall risk their lives by accepting the responsibility of fighting witches. Invisible to human eyes, witches are catalysts of despair in the areas they inhabit. An ally of Kyube, a magical girl named Mami Tomoe, befriends and encourages the two girls to accept the contract. For an unknown reason, another magical girl named Homura Akemi is determined to prevent Madoka from accepting the deal.
A freshman halberd named Harudori Tsugumi, befriends two other meisters, Tatane Meme and Anya Hepburn. All three take part in the NOT (Normally Overcome Target) class at DWMA (Death Meister & Weapon Academy ) and learn to control their powers in order to overcome their difficulties to have a normal life, as opposed to the battle-oriented EAT (Especially Advanced Talent) class taken by Maka, Soul, and their companions.