Here is a page for Madoka's history in the franchise's media.
Puella Magi Madoka☆Magica[]
Meeting Homura, Mami and Kyubey[]
Madoka has a dream about a girl fighting a weird creature and a cat-like fairy asking her to become a Magical Girl. She then wakes up and interacts with her family before having breakfast with them. She leaves for school with Sayaka and Hitomi to find out that the girl from her dream transferred to her class who introduces herself as "Homura Akemi". At break, she is asked by Homura to show her the way to nurse's office. However, at their way, Homura tells Madoka some cruel things as that if she loves her family and friends, she must not change.
After school, she visits a cafe with her friends for lunch. Afterwards, Madoka and Sayaka visit a CD shop. When Madoka and Sayaka try some headphones, Madoka is contacted via telepathy by an unfamiliar voice. The voice eventually leads her to the shopping center's basement where she meets the cat-like fairy from her dream. Homura tells her not to touch the fairy but she escapes with Sayaka and the injured fairy only to be trapped at a Labyrinth. However, they were saved in time by Mami Tomoe, a Magical Girl from their school who defeats the Familiars in no time. Homura goes away as she didn't manage to murder Kyubey. Kyubey is healed by Mami and then asks Madoka and Sayaka to become Magical Girls.Episode 01
Following Mami in her Witch hunting[]
After the previous events, Mami takes Madoka and Sayaka to her house and are told about the Magical Girls. The next day, Madoka starts considering to become a Magical Girl but she can't find something she desires very badly. They are again approached by Homura at the school's roof asking her about the advice she gave her yesterday. After school, the girls meet at a cafe and then track the Witch at an abandoned building. Madoka, Sayaka and Mami enter Gertrud's Labyrinth and Mami defeats the Witch.Episode 02
Sometime later, Madoka and Sayaka keep following Mami to her adventures even though Madoka hasn't decided on a wish. The same day, she has a chat with Kyubey about her becoming the strongest Magical Girl that has ever existed. The next day, Madoka and Sayaka after leaving Mitakihara General Hospital spot a Grief Seed on it. Madoka runs to find Mami and later both get into the Labyrinth. Madoka and Mami reunite with Sayaka and Kyubey and witness Mami beating the Charlotte and then the Witch eating her head. Madoka is shocked by this event.Episode 03
Puella Magi Oriko☆Magica[]
Madoka appears in chapter 3, asking Homura to go home with her, along with Sayaka and Hitomi. She isn't aware of Magical Girl system. In chapter 4, she goes for snacks after school with Sayaka, Hitomi and Homura.
In chapters 5 through 7, Mitakihara Middle School 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 Labyrinth 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. Oriko 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 Labyrinth is lifted, Hitomi and Sayaka are seen mourning for Madoka.
In the final chapter of Sadness Prayer, Ultimate Madoka appears before Oriko and Kirika after both of them die at the end of the manga.
Puella Magi Kazumi☆Magica ~The Innocent Malice~[]
Madoka's silhouette appears once during Juubey's explanation about the Magical Girl system during chapter 2.
Puella Magi Tart☆Magica: The Legend of "Jeanne d'Arc"[]
Madoka appears in the last chapter, as Ultimate Madoka when Melissa de Vignolles tells Eliza Celjska that her preach about Jeanne d'Arc being saved and redeemed in the future will be possible.
Magia Record: Puella Magi Madoka☆Magica Side Story[]
Madoka first appears with Sayaka in a flashback of Mami in episode 10.
In episode 14, Madoka makes her first major appearance. In Mitakihara, Witches have gotten a lot stronger and only Madoka, Sayaka and Homura are left to defeat Witches in said city. Madoka along with the other two girls, try to beat Patricia, but escaped her. Madoka then learns the truth behind Magical Girls by Kyubey shortly after the three escaped. Madoka tried to calm down Sayaka who was suspicious of Homur and agressive towards Kyubey but didn't achieve. The next day at school, Madoka notices Sayaka is absent. The same day in the evening, she finds out Homura jumped into Patricia's Barrier, trying to defeat her herself. Madoka comes to help her, while she also tries to cheer up Sayaka through telepathy. Madoka jumps into Patricia's Barrier with Sayaka arriving shortly. The three finish of the Witch together and Madoka is happy about that, since their next move is to visit Kamihama for Mami and Kyoko.
In episode 24, Madoka and the rest of the Holy Quintet have a short scene focused on them trying to defeat Walpurgisnacht. In episode 26, it is shown that Homura travels back time, but there is no confirmation of Madoka's fate.