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.

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.

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.

Source: ANN

Note: The first two films are a compilation of the television series and the third film is an all-new story. Urobuchi Gen said that the third film's story coincidentally matches the lyrics to Kalafina's television ending theme song Magia if one examines them carefully.

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Alternative version: Mahou Shoujo Madoka Magica
Other: Mahou Shoujo Madoka Magica: Concept Movie
Sequel: Gekijouban Mahou Shoujo Madoka Magica: Walpurgis no Kaiten