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Background
Homura's backstory was revealed in episode 10. She was a transfer student who was hospitalized for a long period of time due to heart disease. The whereabouts and status of her family is unknown, as they are never mentioned in the series. In the original timeline, Homura at this point is physically frail and weak most likely due to her illness. She wears glasses and braided hair in her early insecure depiction shown in episode 10. Later in that episode with renewed determination she undoes her braids and uses her soul gem to correct her vision and to heal her heart condition. From then on she no longer required the use of glasses.
Anime
Homura's time-loop officially starts on the 16th of the month in the anime (speculated to be sometime between March and April). She was released from the hospital on the 16th, and transferred to Mitakihara Middle School on the 25th. In the original timeline, she is attacked by a witch and saved by Madoka and Mami. Sometime during the next month, during Walpurgisnacht, she becomes a magical girl while wishing to redo her meeting with Madoka, thus gaining the power to pause and/or rewind time one month.
It is estimated Homura repeated the same month starting on the 16th nearly 100 times before the present timeline in the TV anime. Within these timelines, Homura was able to gradually improve her abilities and acquire items (such as ammunition and weapons from the Japanese military) to prepare for the battle with Walpurgisnacht. She was also able to memorize and deduce through statistics the major events that would occur within all timelines, giving her incredible knowledge about most of her adversaries. The corollary, however, was that Homura experienced the deaths of many of her friends repeatedly, often horrifically. As a general trend, Homura became increasingly distant to Madoka with each repeat of the month.
By the timeline of the TV anime, Homura appeared as a cold and calculating character who is distant from all the characters. She failed to save all of her companions (apart from Madoka), and by Walpurgisnacht, was forced to face the witch alone. She was subsequently defeated by Walpurgisnacht, and seemed just about to succumb to despair before Madoka appears and rewrites the universe with her wish.
After Madoka's revision of the universe, Homura is the only known character to retain her memories of the previous universe. She has possession of Madoka's ribbon, and has a new black bow as her weapon similar to Madoka's weapon. It is unknown if she retained her abilities to manipulate time and space. Homura is shown to have a much closer relationship with Kyubey, so much so she even confides an entire account about how the old universe worked. She also has the ability to create wings of energy, forming angelic wings when confronting Wraiths in the city, and jagged dark wings when walking through the desert.
Wraith Arc
Homura appears in the first pages of chapter 1 in flashback. She is shown saying her goodbyes to Madoka as in the last episode of the anime, with Madoka promising to meet her again and giving Homura her ribbons. She doesn't appear again until the end of chapter 2 after Sayaka has been led away by the Law of Cycles and Mami and Kyoko are standing at the station. Homura is introduced as the new transfer student and she leaves the class in order to meet with Mami and Kyoko on the rooftop, Homura wiping away a tear as she remembers meeting Madoka for the first time. They tell Homura about the giant wraith that has been seen lately and agree not to hunt it on their own. After several days of combing the city for the giant wraith and hunting down other more common wraiths, Homura has a short discussion with Kyubey about Madoka and the previous universe. Soon after, she encounters the giant wraith alone and attempts to defeat it herself by unleashing a large arrow of magic at it which takes on the form of a bird. However the giant wraith withstands the attack and is able to surprise Homura and overwhelm her, stealing a portion of her power. A smaller wraith steals Madoka's ribbon from her as well.
After a nightmare, Homura wakes up in Mami's apartment, with Mami bringing her a tray of tea and many lecturing words. She asks Homura to transform into a magical girl, which she does successfully, and then to summon her weapon, which she cannot. Mami concludes that the wraiths stole a portion of Homura's power but has no idea on how to retrieve it. Homura is impatient to go and retrieve her powers, but Mami cautions her to play it safe and leave everything up to her and Kyoko. Homura alters her memories slightly before thanking Mami and leaving. In the city, Homura talks with Kyubey about the memory-manipulation magic she now has and her lack of time-stopping ability. She takes off to search the city when Kyoko runs into Homura while patrolling the streets. She assures Homura she won't tell Mami she saw her up and about knowing Mami would only lecture her further. When asked why she remains in the city despite Sayaka having disappeared, Kyoko responds she is still here to avenge Sayaka. Kyoko agrees to help Homura in finding and defeating the wraith provided she is the one to give the final blow.
Despite using grief cubes, Homura finds her magical power has yet to recover which Kyubey explains is due to her soul gem's lack of capacity after the wraiths stole some of her power. As Homura sits in the park at night, Kyoko walks up to her telling her she's found a clue about the wraiths. Before Homura can come closer, Mami appears and fires at Kyoko, revealing her to be another mutant wraith that had taken on the form of Kyoko with the intent of attacking Homura. Mami summons several muskets and together her and Homura are able to hold off the wraiths but not for long. During the fight, Homura realizes the wraith is using time-manipulation magic. After a voice gives Homura advice, the two magical girls are able to overcome the wraiths' time-stopping ability and seemingly defeat the Wraith-Kyoko with Mami's Tiro Finale. After, the real Kyoko appears and informs them of the fake Sayaka and they agree on rules in order to limit their ability to be taken by surprise by the mutant wraiths. Mami and Kyoko leave, leaving Homura alone. She hears the voice from earlier once more and turns to see Madoka standing before her. However, this is not the real Madoka but a wraith who has taken on her form. She returns Madoka's ribbon to Homura before asking for her help in stopping the giant wraith. The fake Madoka explains how wraiths really work before explaining that the magic they took from Homura corrupted the wraiths, resulting in the mutant wraiths that take on human form. Despite Homura's reluctance in believing her story, she has the wraith follow her back to her apartment. There, Kyubey examines the wraith and confirms it carries a part of Homura's power in her.
After several weeks of searching for the giant wraith, Homura and Wraith-Madoka are no closer to finding the whereabouts of the giant wraith. Wraith-Madoka asks Homura what she really thinks of her since she is taking the form of her most precious friend. Homura snaps at the wraith, telling her she is nothing more than a fake for which Homura holds no shred of emotion for and threatens to kill her for insulting Madoka's wish. But the wraith tells her she is lying to herself and that she is not only a wraith but also Homura's heart.
Mami and Kyoko decide to begin their search from the beginning. Mami is upset to find that Homura had been searching for the giant wraith alone and worries that something may happen to her. Homura snaps at both Mami and Kyoko before taking off. Alone, Homura asks Kyubey what she wished for in order to become a magical girl but Kyubey doesn't know the answer to that. Homura worries that she may have used her memory-altering magic on herself in order to turn her dream of Madoka into memories instead. Wraith-Madoka catches up with Homura and offers to walk her home but not before Mami and Kyoko run into them. However, to Mami and Kyoko the wraith looks nothing like Madoka and only has the form of a mutant wraith wrapped around Homura. They transform into magical girls and prepare to rescue Homura, but Homura instead begs the wraith to save her from being a magical girl. The wraith takes Homura's soul gem and teleports them from the area, leaving Mami and Kyoko behind.
At Homura's apartment, Homura and Wraith-Madoka sit in front of her many monitors and watch as a flashback plays out in which Homura makes her original wish to Kyubey to protect Madoka. Kyubey appears only to admonish Homura for having a wraith eat all of her emotions in order to avoid meeting the Law of Cycles. Outside, the wraiths begin their attack on the city, leaving people dead rather than simply emotionless. As Mami and Kyoko fight their respective battles, Wraith-Madoka and Homura watch from a nearby rooftop. Before the wraiths can bring the final blow to Mami, Wraith-Madoka takes the ribbon from Homura and unleashes several arrows from the air in Madoka's characteristic attack, protecting Mami. The wraith appears as Madoka to even Mami now that she has her ribbon. Together the wraith and Mami are able to work together to take down the two imposters.
By this time the giant wraith has been consumed by the power it took from Homura and transforms into a witch-like creature complete with familiars. The wraith and Mami fight off the familiars but not before Kyoko and Mami are killed by the giant wraith. Wraith-Madoka continues in her struggle to defeat the witch-like wraith alone, but is overwhelmed and soon plummets to her death. Homura watches the battle dispassionately until she suddenly recovers herself and runs to catch the falling wraith. She realizes that Madoka is not a dream as the witch that stands before her is the proof that Madoka existed.
Homura regains her original memories. Upon arriving to the new universe, she discovered that her time-manipulation shield no longer worked and she initially discarded it only to have the shield open a small portal to another world. Homura jumps into the world inside her shield and discovers Kriemhild Gretchen inside. Before she can destroy the shield, she realizes that if a witch is inside her shield then Madoka may also be inside fighting the witch. Instead, Homura used her magic to alter her own memories and causes herself to forget the existence of the time shield.
After Homura and Wraith-Madoka land on the streets below, Homura reaches for the ribbon the wraith is holding and finds herself transported to another world. Her appearance changes to her original appearance with glasses and braids. There, she meets a doppelganger of herself who introduces itself as the personification of Homura's power that was stolen by the wraiths. It explains they are inside the world of her soul gem and that it was freed when the wraith that housed it was destroyed. After being stolen by the wraiths, her magical power was able to take control of one of the mutant wraiths in order to assist Homura. Homura asks her magical power what caused the wraiths to go rogue and her magic explains that it was due to the time manipulation magic coming from another universe with different laws. When Madoka and Homura parted ways in the space outside of the universe, their feelings for each other were so strong that a true miracle occurred and their feelings crystallized into a new soul gem for Homura. Because a miracle was granted to a magical girl without a normal exchange, it became separate from the laws of the universe and was considered in incomplete magic. After some time, this new magic began to interfere with her original magic, causing her shield and Madoka to suddenly link up. After Homura erased her memories of the shield, the wraiths stole the shield and were consumed by the curses that were contained within. Because the curses were a form of emotional energy not known in this universe, it corrupted the wraiths and caused the giant wraith to become a witch destined to destroy the world. Homura's thoughts take on the form of Sayaka, Kyoko and Mami who voice her self doubts in having rewritten her own memories rather than lose the shield and her proof of Madoka's existence. Homura takes off her glasses and undoes her braids, filled with a new resolve to protect Madoka even at the cost of her shield. She asks her magic to lend her power once more and her magic power takes on the form of her soul gem.
Filled with power once more, Homura unleashes several hundred arrows that destroy the smaller wraiths and familiars before firing a single large arrow at the witch. As she drives the arrow further in, the witch cracks open and reveals the face of Kriemhild Gretchen and her shield inside. As Homura reaches for her shield, the witch uses its power to stab Homura through several times in an attempt to stop her. But Madoka appears before Homura and helps push her the last few inches towards the shield. As Homura touches the shield, it crumbles to pieces and the witch is obliterated. Back inside her soul gem, her magical power incarnate holds a sleeping Homura in her hands as she explains that Madoka has reset the timeline of this universe in order to prevent the curses of the previous world from interfering. Unlike last time however, Homura will lose her memories of the previous timeline.
Homura snaps to alertness as she realizes she is standing at the station with Mami and Kyoko, Sayaka having just been led away by the Law of Cycles. Some time later, Homura is having the same discussion with Kyubey concerning Madoka and the previous universe. As Homura drops down to destroy the wraiths in the streets below, Kyubey reveals a piece of Homura's shield it managed to salvage and explains how he kept his memories of the previous timeline. Now that he has a piece of the shield and proof of Homura's story concerning the Law of Cycles, he and the other Incubators can now plan for a way in which they can capture Madoka.
The chapter ends as Homura is walking in the desert, ready to take on a hoard of wraiths as several Incubators watch from atop some nearby ruins.
The Rebellion Story
In events prior to The Rebellion Story Homura was captured by the Incubators, and her Soul Gem was placed in an Isolation Field that blocked out the Law of Cycles. This strain led Homura to transform partially into a witch without her knowledge. In this form, she also unconsciously created a labyrinth that was a near-perfect replica of Mitakihara City, and unconsciously lured her former acquaintances into it. She even drew in Madoka from the Law of Cycles, who entered the barrier along with Sayaka and Nagisa Momoe. In this dream world, Homura unconsciously distorted almost everyone's memories (including her own) so that they believed they were living in the real world fighting new enemies called Nightmares. In order to stop the Incubators from fulfilling their goal, Madoka entrusted her memories and powers to Sayaka and Nagisa. Sayaka only pretended to have her memories altered, while Nagisa disguised herself as Charlotte/Bebe.
Eventually Homura realizes that she's trapped in a witch's barrier and attempts to discover who is behind it. Near the end of her journey she has a conversation with Madoka that causes her to realize that she can't accept Madoka's sacrifice. At this point she begins to realize she is the witch, and confirms it when she separates herself from her Soul Gem without consequence.
At this point Kyubey appears and explains the truth about Homura's present nature and the Incubators' plan to control the Law of Cycles. This causes Homura to go berserk and curse her existence, completing her transformation into a witch known as Homulilly. Madoka and the other magical girls manage to rescue Homura by destroying the stasis field containing them all, returning them to reality. Due to the Isolation Field, Homura only became a witch inside her own Soul Gem, allowing Madoka to save her.
Ultimate Madoka arrives to take Homura away as per the Law of the Cycle. However, Homura grabs Madoka first. Her Soul Gem turns black, then fills with swirling colors that Nagisa calls worse than curses. Reality begins to crack as Homura separates Madoka from her goddess self. The colors burst out of her Soul Gem, and both the cracks and colors engulf the entire universe.
Homura and Kyubey reappear in the same place where Madoka ascended in Episode 12. Homura shatters her Soul Gem in her mouth, and a new gem appears called the Dark Orb. Kyubey exclaims that Homura is rewriting the universe, and asks what happened to her Soul Gem. Homura explains that she remembered all of the times she repeated time, and all of the pain she suffered for Madoka's sake. She says that even this pain has become precious to her, tainting her Soul Gem with something greater than curses. As she swallows the Dark Orb, she calls it the pinnacle of human emotions: Love.
Homura transforms into a new form and grows a pair of black wings. Kyubey says that Homura is no longer a magical girl or a witch, and asks what Homura is now. Homura that since she brought down and imprisoned god, it's only appropriate to call her a demon (akuma). Kyubey decides that it was a mistake to experiment with human emotions and flees, but Homura grabs him and says she still needs his existence to deal with all the curses of the world.
Homura effectively becomes a goddess of this new universe. Apart from her true nature as a demon, she still exists with a human form in the real world and can interact normally with everyone else. She appears to have the power to manipulate the memories of virtually anyone she pleases, but otherwise the full extent of her abilities are unknown. It is assumed that Homura is a deity that primarily embodies love (whereas Madoka embodies hope).
Homura is presently holding a fraction of the Goddess Madoka captive--specifically, the part that was Madoka Kaname before she became the Law of Cycles. It is also implied she is placing the world's curses onto Kyubey. Despite proclaiming herself as a demon, Madoka, Sayaka, Kyoko, Mami, and Nagisa are all given happy lives in her new world.
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