Madoka in the Anime
After Mami's death, Madoka changed her mind about becoming a magical girl.
In Episode 6, Junko and Madoka had a conversation on how difficult it is to do the right thing, even when no one is in the wrong (per say). Junko's advice was for Madoka to be on the wrong against her friend to solve the problem, even if it means that her friend would hate her for it.
Episode 8: Kyubey claimed Madoka's power to be godlike, to the point where she could even change the laws of the universe if she wished for it.
Episode 10: In the first timeline, Madoka along with Mami saved Homura from a familiar. She died during the fight with Walpurgis Night. In the second timeline, Madoka turned into a witch for the first time, revealing to Homura the link between magical girls and Witches. In a later timeline, Madoka killed Mami in order to save Homura, as Mami lost control of herself and had just killed Kyoko. This is also the timeline in which Madoka asked Homura to go back in time to prevent her from becoming a magical girl. Madoka's power increased exponentially after every timeline. The first time showed she was an ordinary magical girl. In later timeline she had enough power to defeat Walpurgis in one shot, was capable of destroying the entire planet within 10 days in her witch form, and satisfied all Kyubey's energy quotas of the Earth.
Episode 11: Junko confronts Madoka to stop her from getting into the danger of the storm, Madoka reminds her mother that she is a good girl and never does anything wrong but she tells her she needs to do this, a throwback to their earlier conversation. Madoka knows that what she is doing will worry her family, but she also knows that she must disobey her mother to save her family and her town. This conversation between Junko and Madoka earns her mother's trust.Homura's time repeats had linked multiple parallel universes together with Madoka's fate as their center. With every reset, Homura would force yet another parallel universe to be centered around Madoka. The accumulated karma is the reason why Madoka's potential power is so great. Hearing the revelations from Kyubey regarding the history of Magical Girls, Madoka was deeply hurt and thus wanted to save these girls from despair.
Episode 12: Madoka wished to erase all witches in every dimension, in every timeline, with her own hands. This created a paradox because Madoka would eventually erase her own witch self, while she must continue to exist and destroy other witches. This paradox resulted in Madoka escaping the bounds of reality and ascending to godhood as Ultimate Madoka. Since Madoka never existed as a human in this new reality, she is no longer remembered by anyone, except for Homura, and Tatsuya for some reason. Sayaka also remembers her after she passes on and becomes a part of the Law of Cycles, as Sayaka confesses to her in episode 12 that she has caused her best friend a lot of trouble; this could be interpreted as Sayaka having learnt of her unfortunate fate of turning into a witch in the other timelines, an outcome which clearly inflicted a great deal of emotional hurt on Madoka.
Wraith Arc
Madoka only makes a few small cameo appearance in Wraith Arc. In the beginning she is seen bidding farewell to Homura and giving her her ribbons. In chapter 2 she is seen taking Sayaka once she's used up her magic and in Chapter 9 she is seen helping Homura to destroy the time shield and resetting the timeline so the curses of the previous universe don't interfere with the current one.
A mutant wraith disguises itself in Madoka's form and helps to assist Homura throughout the story, even going so far as to join in the battle against the mutant wraiths.
Rebellion
At the end of the anime, Madoka becomes known as the Law of Cycles - the power that brings salvation to magical girls. However, Homura tells Kyubey about the witch system, and Kyubey decides to use Homura's Soul Gem in an experiment. Kyubey places Homura's Soul Gem in an Isolation Field - a space that blocks out all external influence, including the Law of Cycles. However, the Isolation Field prevents Homura from being born as a witch, meaning that Madoka's wish is not invalidated. (Although not directly stated, its implied that by creating a space where the Law of Cycles cannot enter, Kyubey blocks Madoka's omniscience.) Ultimately, a witch barrier forms inside Homura's Soul Gem. Kyubey allows the barrier to draw in victims, including Mami, Kyoko, and Madoka's family. Kyubey believes that this will eventually cause the Law of Cycles to materialize in the barrier. Kyubey's goal is to observe the Law of Cycles, which would ultimately allow him to interfere with and control it.
However, Madoka is aware of Kyubey's plan. She enters Homura's barrier with Sayaka and Nagisa Momoe (the magical girl who became Charlotte). Sayaka and Nagisa are now part of the Law of Cycles and are capable of invoking the power of their witch forms (since their witches were also absorbed by the Law of Cycles before they were born.) Madoka entrusts them with her memories and powers in order to fool Kyubey, and allows Homura's barrier to alter her memories and suppress her powers.
Within Homura's barrier, Madoka believes that she is an ordinary magical girl. She is reunited with her family, who were also taken into Homura's barrier and had their memories altered. Along with Sayaka, Kyoko, Mami, and Bebe (a disguised Nagisa), Madoka fights Nightmares, monsters created by Homura's barrier. Kyubey recognizes Madoka as the Law of Cycles but is unable to determine the nature of her powers. He decides to stay close to Madoka, pretending to be a harmless animal-like helper. Eventually Homura appears in her barrier and joins the other magical girls. Homura is unaware that she is a witch, but she soon realizes that she's in a witch barrier and resolves to discover the truth.
Homura's journey brings her into contact and conflict with the other magical girls. Madoka comes to Homura and offers to listen to her problems. Homura tries to tell Madoka about her fate at the end of the anime, framing it as a dream she had. Madoka tells Homura that it sounds like a bad dream, and reassures Homura that she would never want to go away to a place where she can't see anyone again. Homura then believes that Madoka isn't happy being the Law of Cycles(or isn't as happy as she could be), and exclaims that she have stopped Madoka from sacrificing herself. Homura then decides to believe that Madoka is real (having wondered if Madoka was an illusion), and begins to realize that she herself is the witch.
Ultimately, Homura learns about Kyubey's plot, and decides to foil it by dying in her barrier. Homura transforms into her witch form, Homulilly, and marches to her death. Fortunately, Sayaka and Nagisa have explained everything to the other magical girls, and they have a plan to save Homura. Sayaka summons her witch self Oktavia and an army of familiars. Madoka and Nagisa use their magic to attack the ceiling of Homulilly's barrier, while the other magical girls, the summoned familiars, and Oktavia hold off Homulilly and her army of familiars. Ultimately, Madoka destroys the ceiling of the barrier, revealing Kyubey's Isolation Field. Madoka then reaches out Homura's humanity and the two girls combine their powers to destroy the Isolation Field from the inside, completely foiling Kyubey's plan.
With the Isolation Field destroys, all the magical girls reappear in the real world. Sayaka and Nagisa return Madoka's memories and powers to her and she transforms into Ultimate Madoka. However, Madoka is still in a human form (which means she lacks omniscience and can be seen by others). As she comes down to take Homura's Soul Gem into the Law of Cycles, Homura grabs Madoka's hands before her Soul Gem can be purified. Homura's Soul Gem turns black, and then fills with a new color. (It's unclear if this color was something that had already existed in Homura's Soul Gem, or if it is the result of Homura grabbing Madoka and interfering with the Law of Cycles). Homura's actions causes reality to crack. Madoka is then separated from Ultimate Madoka (it is unclear if Homura deliberately caused this, or if it is the result of Homura's interference). The colors inside Homura's Soul Gem explode outward. The cracks perpetuate throughout reality, followed by the colors of Homura's Soul Gem, which engulfs the universe.
Homura has now become a new existence, which she defines as a demon. She explains that she took a piece of the Law of Cycles, which corresponds to Madoka's existence as a person before she became the Law of Cycles. Homura creates a new world where the magical girls can be alive and happy, although she alters their memories to fit with the new world. In this new reality, Madoka believes she has spent three years in America with her family, and they have just moved back to Japan. Madoka transfers into her class from the original reality, reversing her role with Homura's. Homura introduces herself to Madoka and offers to show her around the school. As they walk together, Homura asks Madoka how she feels returning to her hometown. Madoka says it feels familiar, but something feels different. As the keep walking, Madoka realizes that the thing that feels different is herself. Her eyes glow gold, her yellow hair ribbons untie themselves, and reality changes. Homura grabs onto Madoka and says that Madoka is her true self right now, returning Madoka and reality to normal. Homura asks Madoka if she thinks the world is precious, and if she thinks either laws or desires are more important. Madoka thinks that law is more important, saying that selfishly breaking the law is a bad thing. Homura takes off the hair ribbon she received from Madoka and says that she and Madoka might become enemies someday. She ties the ribbon into Madoka's hair, saying that she doesn't care about being Madoka's enemy as she just wants a world where Madoka can be happy. In one of the final scenes of the movie, Madoka is shown happily unpacking boxes with her family.
Drama CDs
From Drama CD 1 "Memories of you", the reason Madoka became a Magical Girl in the first timeline is to save a cat which had been run over by a car. Madoka also treated Homura very nicely from the beginning, who at that time was being bullied. We also learn that whenever Madoka made a contract and become a Magical Girl, she would act much more confident since it gave her a sense of purpose. Madoka's kindness in this first timeline towards Homura is one of the major reasons why Homura is so drawn to her. Homura's interventions during the course of the anime prevented this change.
In the Drama CD 2"Sunny Day Life" Madoka used to get good grades, but her duties as a magical girl are interfering with her studies. For what is worth, Madoka's grades are still better than Sayaka's.
The Different Story
Madoka first appears at the very end of volume 1, waking Mami up in her apartment in order to get her help stop Kyoko and Sayaka's fight. She has not contracted yet in this timeline, but accompanies Mami and Sayaka on their witch hunts.
Madoka is worried about Sayaka, and always thinks how to help her. She tells Kyousuke about how his wrist was healed with Sayaka's wish. This doesn't help Sayaka in the end, however.
Madoka makes her wish to revive Sayaka and becomes a magical girl at the very end of this story, this causes Homura to give up on this timeline. Madoka doesn't know the truth about the magical girl system. She thinks Sayaka was killed by witches because Homura told her so. Madoka meets Kyoko after being helped by her and Homura. They become friends secretly and tell each other about another side of Sayaka and Mami.
Kazumi Magica
Madoka's silhouette appeared once during Juubey's explanation about Magical Girl system. She also makes a single-panel cameo in the extra pages in the first volume of the collected edition.
Oriko Magica
Madoka appears in Chapter 3, asking Homura to go home with her, along with Sayaka and Hitomi. She is well protected by Homura and isn't aware of Magical Girl system.
She appears in Chapter 4 for one page. She is shown with her friends Homura, Sayaka and Hitomi going out for snacks after school.
In chapters 5 through 7, Mitakihara Junior High is attacked by Oriko and Kirika. Oriko speaks to the school through the school's broadcast system, and seems to give a threatening look to Madoka as she claims she will defeat a creature of ultimate despair that will descend upon them. As a witch's barrier forms over the school, Madoka is separated from her friends attacked by familiars. Homura saves her in time, but Madoka demands to know why she does not help the other students. Homura knows she cannot save everyone, and wanted to try to save Madoka anyway. Madoka apologizes as Homura puts her in a protective barrier so familiars cannot attack her and leaves to defeat the perpetrators. Madoka escapes from the protective barrier created by Homura and tries to help Homura with Sayaka and Hitomi. Madoka was Oriko's real target. The white magical girl wanted to kill her before she could contract and become a magical girl herself, and then the most powerful witch ever. She is killed by Oriko at the very end. Oriko uses a shard of Kirika's witch body to impale Madoka through the torso. Once Oriko dies and the witch barrier is lifted, Hitomi and Sayaka are seen mourning for Madoka.
In the final chapter of Sadness Prayer, Madoka appears in her goddess form before Oriko and Kirika after both of them die at the end of the manga.
Tart Magica
Madoka appears in the last chapter (Chapter 21), as Ultimate Madoka when Melissa de Vignolles tells Eliza Celjska that her preach about Tart being saved and redeemed in the future will be possible.
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