Rebellion — Madoka used to be a normal girl living happily. This all ended when she sacrificed herself in order to save other magical girls from the utterly cruel fate that awaited them. Unable to let her memories of Madoka die, Homura continues to fight alone in the world that Madoka left behind for humanity in order to see her smile once more.

Eternal — Madoka learns from Kyuubee, whose real identity is Incubator, that his species makes contracts to make girls into magical girls that inevitably become witches in order to use the energy that spawns from their despair to counter entropy in the universe. Kyouko, hoping for a chance that Sayaka can be made human again, takes Madoka with her to try and reach her humanity. This ultimately fails, with Kyouko choosing to sacrifice herself to destroy Sayaka with her. Meanwhile, it is revealed that Homura comes from another timeline, having relived the same month several times in the hope of saving Madoka from a grim fate at the hands of the ultimate witch, Walpurgisnacht. Homura attempts to face Walpurgisnacht, but is ultimately defeated and draws close to despair, feeling her efforts have become pointless. Just then, Madoka appears and uses the built up energy from several timelines to become a powerful magical girl capable of eliminating witches before they are born.

Beginnings — In the city of Mitakihara, Kaname Madoka, along with her friend, Miki Sayaka, encounter a creature named Kyuubee and are saved from witches by magical girl Tomoe Mami. Kyuubee offers Madoka and Sayaka the chance to have any one wish granted in exchange for becoming a magical girl and fighting witches, whilst Akemi Homura, another magical girl and recent transfer student, is strongly against Madoka becoming one. Before Madoka can make a decision, however, Mami is killed by a witch, leaving Madoka too afraid to become a magical girl. Sayaka, however, decides to become a magical girl herself in order to heal the hand of her childhood friend, Kamijou Kyousuke. As Sayaka soon comes into conflict with another magical girl named Sakura Kyouko, they, along with Madoka, learn the shocking truth that their Soul Gems, the source of their magical powers, literally contain their souls.

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.

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.

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 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.

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 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.

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.

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.

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.

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?"

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