She has a loving family and best friends. She laughs and cries from time to time. Madoka Kaname - an eighth grader who lives such a peaceful life. 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. She looks exactly the same as the girl Madoka saw in her dream.

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. She speaks of what it means to have been chosen by Kyubey, the purpose of a magical girl, and the existence of witches. Of a chance to make any wish come true, and the cruel mission that waits. Mami suggests to the anxious two girls, Why don't you come with me to wipe out the witches.

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?" Mami warns sternly, "You need to know the intent of your wish more clearly if you want to make it for another person." The next day after school, Sayaka goes to see Kyosuke with Madoka. On the way back, they happen to discover a Grief Seed about to hatch in the hospital parking lot. If left alone, it could turn into a huge disaster. Sayaka and Kyubey stay to guard it, as Madoka runs to get Mami.

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. That evening, Madoka visits Mami's room. On the way back, she comes upon Homura at the condominium entrance. The two of them walk side-by-side in the sunset. Homura talks about the reality of dying as a magical girl. Madoka offers heartrending kind words.

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. Madoka, however, feels unsure of herself since, although she made the decision to become one before Sayaka, she ultimately gave up on becoming a magical girl. Kyosuke's parents, primary physician, and the hospital staff gather on the hospital rooftop to celebrate the recovery of his hand. His father returns his favorite violin to him. Kyosuke hesitates at first, but begins to play and his unchanged genuine talent enraptures everyone. Watching Kyosuke, Sayaka enjoys supreme bliss. Meanwhile, Kyoko is watching Sayaka's movement on the hospital rooftop from an observation deck.

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. The next day, Sayaka and Madoka search for a trace of the Witch's Familiar who slipped away during Kyoko's intrusion. Looking over the scene of the battle, Madoka suggests a peaceful resolution with Kyoko, but Sayaka has made up her mind to fight to the death in this battle between magical girls. While they argue, Homura makes contact with Kyoko at a game arcade with a proposal.