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.

While rescuing Kyubey from being attacked by Homura, Madoka and Sayaka lose their way in a mysterious space. They find themselves in a desperate situation and are rescued by Mami Tomoe, a magical girl. Afterward, Mami invites them to her room.

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.

As a magical girl, Sayaka rescues Madoka and Hitomi from a witch. Now that her wish has come true by signing Kyubey's contract, her mind is clear and she doesn't seem to regret becoming a magical girl.

Homura appears suddenly on Sayaka and Kyoko's battlefield. She intervenes and knocks Sayaka unconscious with a single blow. After seeing this, Kyoko is on her guard against Homura, and leaves, putting an end to the battle.

Sayaka discovers the truth about her own body as a magical girl. She wavers between the wish that came true by accepting the destiny to fight and the high price she paid for it. Sayaka is in low spirits at home when Kyoko Sakura shows up.

Despite her own injury, Sayaka keeps shredding the witch in front of her. Thanks to healing magic, she wins without a scratch at the end. But she seems extremely exhausted.

Sayaka's Soul Gem turns into a jet-black grief seed, which hatches and a new witch emerges. Carrying Sayaka's body, Kyoko focuses on defending against the approaching witch's attacks. Homura cuts into the witch's labyrinth and leads Kyoko to escape.

A scene depicting a female transfer student. The timid girl is so nervous and meek. She introduces herself shyly while feeling the eyes of all the students in the class. At recess, other girls gather around her and ask questions curiously.

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.