Magia Record Story Beginning and Eternal: The Lost Record
Beginning and Eternal: The Lost Record is primarily a retelling of the anime series as viewed and narrated by Ultimate Madoka.
Prologue
Ultimate Madoka sits in the heavens and listens to the various parallel worlds as represented by musical records. She turns and summons a "Great Door" which causes two vortexes to appear before her. She then finds herself in Homura's room, which is filled with various windows. She then summons a key next, which unlocks one of the windows and displays a memory for her.
Record I: A Fateful Meeting
Saotome-Sensei gives her usual lecture on fried eggs versus sunny side-up eggs. She then introduces the new transfer student, Homura Akemi. Madoka introduces herself and then offers to escort Homura to the nurse's office, where she compliments Homura on her name. After school, Homura unknowingly wanders into a Witch's labyrinth and is saved by Madoka and Mami Tomoe in Magia Record. She learns about Magical Girls, Witches, and about Walpurgisnacht. Soon Walpurgisnacht descends and Mami is killed, leaving only Madoka capable of fighting her. Madoka thanks Homura for being her friend then sacrifices herself to destroy Walpurgisnacht. It is then that Homura contracts with Kyubey in order to go back in time and protect Madoka. Homura awakens to find herself in the hospital a week before she transferred schools. However she is holding her soul gem in her hand, so she knows it wasn't all just a dream.
Record II: An Awakened Heart
When school started again, Homura rushed over to where Madoka was sitting and told her she was a magical girl too. Madoka introduces her to Mami, who helps to teach her how to use her time magic offensively. They soon encounter the Witch Patricia, and with the help of their training are able to defeat it easily. Despite training for days on end in preparation for the big battle, Madoka still ended up using all of her magic in the battle against Walpurgisnacht and transformed into a Witch before Homura's eyes. Ultimate Madoka sighs deeply and sadly as she watches Homura learn the truth for the first time.
Record III: An Exchange of Promises
Homura awakens in the hospital once more and resolves to tell everyone that they're all being tricked by Kyubey. However, Sayaka not only didn't believe her, but turned against her. When Sayaka eventually became a Witch, Homura and the others were forced to finish her off for good. Immediately after the fight, Mami used her binding magic on Homura and shot Kyoko's soul gem. She turned her sights on Homura, determined to kill them all rather than let them become Witches. Madoka in turn kills Mami before she can kill Homura. In tears, Homura and Madoka resolve to fight Walpurgisnacht alone.
After Walpurgisnacht is destroyed, both Homura and Madoka were left spent and on the verge of Witchification. Homura wonders if it wouldn't be better for them to both become Witches and destroy everything. Madoka then pulls out a Grief Seed she had been holding onto and uses it on Homura's Soul Gem (implied to be Sayaka's Grief Seed). Madoka asks Homura to go back in time and change it so none of this ever happens. She then asks Homura to kill her before she can become a Witch.
Intermission
Ultimate Madoka sighs heavily once more. She wonders if she put too great a burden on Homura by getting her to make that promise to her. She wonders if there wasn't a different way to save her friends from that despair. Ultimate Madoka thinks about each and every event that happened, and as she does so, her expression darkens. She stays deep in thought for some time. Eventually, she stretches her hands out towards the next window and unlocks another memory.
Record IV: The Decision
Knowing that no one will believe her about the future, Homura decides to fight alone and never depend on anyone else, even if it means she has to destroy every last Witch by herself including Walpurgisnacht. At last, Walpurgisnacht appears and Homura attempts to fight it alone. Madoka and Kyubey watch the battle from afar. Madoka contracts and takes down Walpurgisnacht with a single hit, only for her to transform into a Witch after having spent all her magic on that one attack. Homura goes back in time once more and attempts to change Madoka's fate over and over again.
Record V-1: An Accelerating Fate
The timeline begins once more with Homura introducing herself as the new transfer student. As Homura and Madoka head to the nurse's office, Homura asks her if her family and friends are precious to her and warns her to never change. Homura tries to prevent Kyubey from making contact with Madoka, but is unable to do so. Madoka tries to protect Kyubey from Homura, but before Homura can finish Kyubey off, Sayaka throws a fire extinguisher to distract her and helps Madoka to escape with Kyubey. They then finds themselves inside a Witch's Labyrinth.
Record V-2
Madoka and Sayaka are rescued from the labyrinth by Mami. Mami makes short work of the Witch and introduces herself. She offers the Witch to Homura, who insists she stay there. Mami warns her to go once more and Homura obliges. Homura realizes that Kyubey will try to push Madoka to contract and she resolves not to let him.
Record VI-1: The Candy Witch
Ultimate Madoka continues to watch the memories, frowning. When she was human, she could never understand why Homura viewed Kyubey as the enemy. Homura soon senses the magic of a powerful Witch near the hospital. Madoka finds Mami and tells her about the Grief Seed her and Sayaka found at the hospital. Sayaka is inside the barrier with Kyubey keeping an eye on things until Mami can arrive. Inside the barrier, Homura tries to tell Mami to leave only for Mami to bind her with her magic and attempt to take on Charlotte by herself.
Record VI-2
Homura soon finds the magic binding her in place has dissolved. She hurries to the heart of the labyrinth where she finds Sayaka and Madoka trembling in fear. Kyubey urges the girls to hurry and make a contract with him, but Homura steps in and defeats the Witch easily enough. She warns them that this is what it means to be a magical girl. Outside the labyrinth, Madoka asks Homura if she's seen many people die. Homura says yes, and that Mami's body will disappear with the labyrinth. Madoka promises to never forget Mami or Homura.
Record VII-1: The Alliance
Homura worries about driving away and defeating Walpurgisnacht. She knows that if the Witch isn't stopped, then Madoka is sure to contract in order to protect everyone. Despite having gathered a mass of weapons in preparation for the battle, Homura isn't certain she'll be able to defeat it on her own and decides to form an alliance with Kyoko (since Mami is dead). At an arcade, Homura proposes working with Kyoko to defeat Walpurgisnacht. In exchange, Kyoko will be allowed to take over the city as her territory. Kyoko agrees and offers Homura some candy.
Record VII-2
By this point, Sayaka had contracted with Kyubey. Both her and Kyoko would fight and disagree about everything. Homura had been able to stop them from clashing once, but by sheer coincidence they both learned the secret about Soul Gems and how they were their actual souls. Homura realizes she should have kept a closer eye on Sayaka since she knows that Madoka would be willing to contract to save her best friend. Some time later, Homura senses a Witch and tracks it down only to find Kyoko waiting outside the labyrinth while Sayaka fights the Witch inside. Angry and fed up, Kyoko transforms and goes into the labyrinth to fight the Witch herself.
Record VII-3
Homura and Kyoko meet up in Homura's home to discuss their plans for Walpurgisnacht. Kyubey appears and warns them that Sayaka is deteriorating quickly. After telling him to leave, Homura explains to Kyoko that Sayaka's soul gem is heavily tainted and soon she won't be able to cleanse it. Kyoko tracks down Sayaka at a train station. Sayaka lets out her lamentations then transforms into a Witch in front of Kyoko. Afterwards, Kyoko tracks down Madoka and asks her to come with her to try to reason with the Witch that was once Sayaka. Despite Madoka's pleas, Oktavia von Seckendorff continues her attack. Homura arrives only for Kyoko to tell her to get Madoka out of there as she uses up all of her magic to destroy Oktavia. Back at Homura's home, Kyubey tells Homura that Sayaka could never be saved from her fate once she transformed into a Witch and he purposefully led Kyoko there so Homura would be the only one left to fight Walpurgisnacht, thus ensuring Madoka will contract to protect everyone.
Record VIII-1: I Will Never Give Up
Ultimate Madoka has watched every memory up until this point. She closes her eyes and remembers all the girls she had wanted to save, but couldn't. She continues to watch the memories as Kyubey explains that it was thanks to Homura endlessly repeating time that cause the magical potential of Madoka to grow into incredible potential. All of the karmic destinies from all the different timelines have converged on this one timeline.
Record VIII-2
Madoka unexpectedly appears at Homura's home. As she looks around, she realizes that the screens all depict Walpurgisnacht. She knows Homura will have to fight it alone and offers to contract to help Homura. But Homura lies and says she could defeat it by herself all along. Madoka doesn't believe her, but she wants to believe that Homura wouldn't lie to her. Breaking down in tears, Homura tells Madoka she would never believe her because truthfully they aren't even from the same timeline. She tells Madoka that she's from the future and has watched Madoka die countless times. Every time she goes back to try to change the future but to this day she's been unsuccessful. Homura begs Madoka to allow her to protect her.
Record IX: The Decisive Battle
Walpurgisnacht has arrived. Homura attempts to defeat Walpurgisnacht with every last bit of arsenal she has, but no matter what she throws at it it's never enough. Madoka and Kyubey watch on as the battle rages. Kyubey tells Madoka that Homura can't give up because the moment she does she'll despair and turn into a Grief Seed. If she loses she'll negate this timeline and travel back in time over and over again until she succeeds.
Homura continues to fight, but soon realizes she's out of magic and can't stop time anymore. She decides to rewind time once more, but if she does then Madoka's fate will get worse each time. Homura wonders if everything she's done has been for nothing as her soul gem begins to fill with impurities. Madoka tells her that she's done enough, and apologizes for resolving to become a magical girl.
Record X: A Wish
Homura begs Madoka not to contract, telling her if she does then all of Homura's efforts will have been in vain. Madoka apologizes once more for what she is about to do, and promises she will never let her efforts be in vain. She turns to Kyubey and makes her wish to have the power to destroy all Witches before they're born, past, present and future. Madoka then becomes Ultimate Madoka and rewrites the laws of the universe.
Epilogue
Everything that existed in the universe was rewritten, removing all Witches from this world in exchange for Madoka's existence. All proof and memories of her life in this world disappeared without a trace from everyone's minds, except for Homura. In the new universe, Magical Girls had the sworn duty to fight "Wraiths", a new enemy produced by the defects in the universe. Homura cries for Madoka, but Mami and Kyoko don't know who she's talking about.
Ultimate Madoka finishes watching all of the memories, and smiles contentedly. She recalls the worlds she spoke when she was a human girl, promising to never forget Homura. The records continue to spin and sing their songs with the voices of all Magical Girls singing together in harmony, but the records holding Homura's chronicles are nowhere to be found. Ultimate Madoka's wish of hope had overwritten Homura's journey into a world without Witches. Just as Homura was the only one who knew her past form, Ultimate Madoka was the only entity who knew of Homura's past.
It is then revealed that the mysterious place is a secret room inside Ultimate Madoka's heart. It's a special room where she keeps invisible "records" etched deep inside her heart. The memories of Magical Girls connected to her, and the special friend who traveled through time, over and over, to protect her.