Homura Akemi finds herself in a strangely peaceful Mitakihara, fighting nightmare creatures alongside Madoka Kaname, Sayaka Miki, Kyoko Sakura, and Mami Tomoe, all living as magical girls with no memory of how they arrived. As her own memories resurface, Homura starts to notice what does not fit in this city and sets out to learn who built it and why. This sequel film continues directly from the original series' ending.