Um dia, Madoka Kaname tem um encontro mágico que pode mudar seu destino. Este é o início de uma nova história sobre garotas mágicas feiticeiras.

Shiki Tohno is a boy who, after an accident as a child, is able to see strange lines coming from objects and people. He has to wear special glasses to stop seeing them. If he cuts some of these lines, he destroys people connected to them. One day he meets a woman called Arcueid and together they start a journey that's going to reveal some secrets of his past.