Madoka Kaname, an eighth grader who lives such a peaceful life, has a loving family and best friends. She laughs and cries from time to time. One night, she has a strange dream. It was supposed to be an usual routine day, but the arrival of Homura Akemi - a transfer student who came to Madoka's class, changed that.

Madoka and Sayaka are getting used to Mami's witch hunting trial run. Yet their wishes remain undecided. Mami reveals her past to the anxious two girls. Sayaka asks, "Does my wish have to be for myself?"

The day after the fierce battle between Mami and the witch was a normal peaceful day. After what they witnessed, Madoka and Sayaka fully realize the demands of being involved in the magical world, and give up becoming on magical girls.

Sayaka's funeral was held in the rain. Madoka returns home with vacant eyes. She barely says anything to Junko who met her at the front door, and goes into her room. Kyubey appears in front of Madoka, who is lost in her grief, alone.

Homura challenges Walpurgisnacht alone and is seriously wounded. She despairs because she can't win no matter how many times she tries. Her actions are making Madoka suffer even more, and she becomes despondent. Her Soul Gem begins to turn black.