Following Madoka's rewriting of the universe, sacrificing herself and her happy normal days to save all magical girls from the cruel fate that awaited them by wiping witches out of existence, the despair still manifest into creatures known as nightmares. Magical girl Homura Akemi continues to fight alone in the hope that she will be able to see Madoka smile again.

She has a loving family and best friends, laughs and cries from time to time... Madoka Kaname, an eighth grader of Mitakihara middle school, is one of those who lives such a life. One day, she had a very magical encounter. She doesn't know if it happened by chance or by fate yet. This is a fateful encounter that can change her destiny. This is a beginning of the new story of the magical witch girls.