Homura dragging Ultimate Madoka down from divinity despite Madoka begging her to stop was insanely out of character, there's no way that Homura would harm Madoka like that in a million years. But then it hit me, I was right. It was extremely out of character because Homura WOULDN'T do it. But Homura had already turned into a witch, and we only need to look at Sayaka in the classic series to see that turning into a witch messes with your moral compass. Homura would never hurt Madoka, but Homulilly would. After all, just five minutes since she was trying to kill Madoka and company with a familiar army. And because Madoka only saved Homura after the transformation rather than before the transformation like the other girls, Homura as we know her had pretty much aready died and been replaced with a witch-like persona. Nice job breaking it, Kyubey.
This also creates what could be the biggest irony of the series. Homura spends about eight years fighting to save Madoka, only to get turned into a witch and wind up becoming Madoka's greatest enemy.
Actually this fits in with her character. Throughout the series the sole reason for her existance is her desire to protect Madoka, only problem is that a Goddess doesn't need protecting. So her very existence is invalidated. She took away Madoka's divinity and make her helpless to fullfil her desire. It also fits in with her being the Devil to Madoka's God. Madoka is the embodiment of selflessness while Homura is selfish to the core.
Another piece of fridge that makes Homura's ascention to devilhood sensible? Her thoughts upon first witching out in Timeline 3 were her wanting to destroy everything that had ever made her cry or hate, contrasting Madoka who wanted to preserve everything.
In addition, remember that Homura's prime motivation is to protect Madoka, even if Madoka neither needs, nor wants it. She'd just had a long conversation with Kyubey about how the incubators were going to try to pervert Madoka's wish, or possibly even capture and use her for their own ends. Homura fell into despair because her wish was no longer valid. But Kyubey just provided her with the knowledge that Madoka was once again in danger and Homura could do something to protect her. The catch was that Madoka was already caught in the trap. The only thing Homura could do to save Madoka was prevent Madoka from fulfilling her purpose so that the incubators couldn't see how Madoka operated. Homura has always prioritized her definition of Madoka's safety over everything else, but even if she did have a few last shreds of sanity that might have caused her to step away from that edge and trust Madoka, becoming Homulilly probably destroyed those.
During Madoka's transformation, a few things are worth noting:
When she holds her soul gem, the only parts of her body that are "normal" colored are her hands. Fitting, considering Homura steals her powers by grabbing her hands.
It's the only transformation where no runes appear.
While she transforms, a film tape that passes horizontally appears, where there are many Madokas holding hands, probably meaning that she exists in parallel and everywhere. Also aided by the fact that she gets 9 screens showing her.
There's also a glass that breaks during her transformation, showing us how she broke the rules of the original universe.
Also, she hides most of her face, with only her eye showing. It looks a lot like the "all seeing eye", as if she watches everything, like an omniscient god
The "dance" phase of her transformation is modeled after that of an idol singer, which works on a number of levels: she's the focus of Homura's admiration and love (Homura is basically a Madoka fangirl), she brings joy and hope to all magical girls (who serve as her audience) and, tragically, she disappeared completely after a very short period of time after someone else drove her to a height of influence and power.
There's a lot of key and keyhole symbols in the background of her transformation - she's basically the 'key' to Magical Girl Heaven, the Incubators view her as the 'key' to the Law of Cycles, and she's trying to 'unlock' the seal on Homura's soul gem.
Madoka's flip-flop on whether or not she would sacrifice herself as she did at the end of the original series seems a bit strange. Then you realize that this is Madoka without the psychological torment she sustained during the anime that drove her into a corner, and it makes a bit more sense.
With all the Fan Works and Licensed Games and other Spin-Offs, it's easy to forget that the beginning of Rebellion is actually the first animated appearance of all five magical girls fighting together. It's a big deal for a reason.
While the level of seriousness varies, every entry in the Cake Song means something to the character singing.
Sayaka is a raspberry as a nod to Cure Berry and their matching elements.
Kyoko is an apple because it is now her Trademark Favorite Food with boosted significance from The Different Story.
Mami is cheese, Bebe's favorite food. Bebe likes Mami, too, and has eaten her in another timeline.
Homura says she's a pumpkin. A story surrounding the pumpkin involves the origin of the Jack-O-Lantern, in which a man was able to prevent the Devil from claiming his soul by asking him to fulfill a last request, only to trap him with a crucifix. He could neither go to Heaven or Hell afterward. Some fans have pointed out the Dark Orb's shape resembles a pumpkin.
Alternatively, Homura's a pumpkin because she's really a witch.
Madoka says that she's a melon, split to bring sweet dreams. Now, what happens in the ending of the movie? Madoka is split from Ultimate Madoka and forced to return to her human form, though there is still an uneven connection to her goddess powers.
At the end of the movie, from Madoka's power, a 'sweet dream' - Homura's new world, in which everyone is happy was truly created...
The line they each use to describe the cake and pass the song onto the next singer is equally significant:
Bebe starts with "Is the cake Sayaka?" Bebe is Nagisa; she and Sayaka are the only ones who actually know what's going on because they're agents of Ultimate Madoka. No one can understand what Bebe says, but Sayaka picks it up easily nonetheless.
Sayaka passes with "The cake is red" to Kyoko, whose theme color is, obviously, red.
Kyoyko passes with "The cake loves Bebe" to Mami. Apart from just being true in general, Mami really does care about Bebe, and she and Homura come to blows over it later on.
Mami passes with "The cake goes around in circles" to Homura. She has no reason to know that. As far as Mami ought to know, there's only ever been one timeline; this is a hint that Mami's memories have been manipulated by Homura, because only Homura would know about her time-looping.
And Homura passes with "The cake is sweet" to Madoka. D'aww. None of the other girls should know anything about Madoka at all, so having anyone but Homura pass the song to her would crack the illusion.
One of the last lines in the song: "on the table/platter is a cat's dream". Homura's barrier is part of a larger scheme by the Incubators to trap Ultimate Madoka within their isolation field, and Kyubey has been likened to a cat...
We later see Homura's body laid out on a funeral altar. She's literally on the table and, as the only magical girl capable of proving the existence of Madoka, she's a dream-come-true for the Incubators who want a bigger energy yield.
Speaking of the song, that scene seems to echo back to episode 3 of the anime, and especially to the first movie's rendition thereof: a bunch of girls sing a cute-yet-disconcerting song about food, then Charlotte proceeds to eat the "food" in question.
The entire scene itself is about as weird and random as it gets, even for a Magical Girl movie. It's one of the first clues that something is amiss in the setting. After all, people usually see weird and random things whenever they are having a dream.
Even the accompanying hand gestures can be interpreted as symbolic, but this time in reverse:
Sayaka covers her face with her hands. Madoka's eyes were metaphorically covered by Homura for most of the series.
Kyoko taps her fingers in a rhythm on the table, as musicians — like Sayaka's crush — are wont to do.
Mami puts her hands together in prayer. Kyoko's wish centered around her father's church.
When it's Homura's turn, the camera pulls away from her and focuses on Kyoko and Sayaka. Mami had less screentime than both of them, only appearing for 3 episodes.
The camera also makes it difficult to see what Madoka is doing, but she also appears to cover her face with her hands. This could be interpreted as Homura's true motive being unknown for most of the series.
And then there's the fact that it's... well, a song about who the cake is. Charlotte's theme is "Wo ist die kase", which is usually translated as "Where is the Cheese?", but the cheese that Nagisa's wish centered on was a cheesecake. It's a callback to Charlotte's labyrinth.
Madoka had the power to remake the universe as the raison d'être for countless timelines. She wasn't the only one. All of Madoka's massive karmic potential was just riding Homura's wake.
Equally brilliant is the call-back to the original series (and consequently the previous movie). When Kyubey discusses the reasons behind Madoka's huge magical girl potential, we see a shot of her with her body tied onto various strings, representing Homura's various timelines. When Kyubey pins the blame on Homura, we see the same shot with Homura replacing Madoka. That's a really long-shot foreshadow, if not a downright lucky coincidence.
In Episode 6 of the series, Kyoko tells Sayaka that, if she wants Kyosuke, she should "break his arms and legs so bad he'll never be able to use them again. Make him so helpless he won't be able to do anything without you. Do that, and this time, he really will be yours and yours alone. Both his body and heart will be all yours." In the end of the movie, although Homura doesn't do this literally, she does cripple Madoka by depriving her of her godhood and memories, trapping her in a Gilded Cage.
After the bus scene, the next we see of Kyoko is her in the arcade, in her casual outfit from the series, playing a dance game. This could probably mean that she's quit school and gone back to her old time-wasting habits since she and Homura found out that they're in a fake world, and have had their minds tampered with to fit in.
In this world, Kyoko and Sayaka have formed some sort of relationship. They even live together. The reason Sayaka doesn't make a fuss over Kyoko skipping school is because Sayaka has known that the world is fake to begin with and she realized that Homura and Kyoko have figured it out.
If one pays really close attention to the details in the beginning sequences, it's easy to tell it's a world of illusion made by Homura. Madoka's hair when down is longer in the movie than in the beginning of the anime, alluding to Ultimate Madoka. Similarity the classroom was a lot more golden in the movie. When Homura enters, she is confident rather than shy but still her moe self, alluding to the fact that she wants to be confident but not the ultimate protector. On hindsight it gives us a really good insight on Homura's psyche.
At the conclusion of their battle with a Nightmare, the magical girls have to sing to it. They all sit in a circle and sing a cutesy, repetitive song about cake and fruit. It seems completely silly and ridiculous—Madoka isn't a musical!—until you realize it's a lullaby. Only natural that you'd need one to defeat a Nightmare.
The same goes for the first Nightmare fight: while the girls don't sign themselves, the lyrics for the song "Not yet" are very much akin to that of a lullaby.
Remember in episode 6 of the anime when Madoka asks her mother for advice about how to help Sayaka? Junko tells Madoka that doing the right thing doesn't always create a happy ending, and suggests that Madoka do something wrong for Sayaka. Junko also warns that it won't be a neat and tidy resolution, and that Sayaka might misunderstand Madoka's intentions. Now apply this to the ending of Rebellion. Homura believes that Madoka's self-sacrificial ascension is keeping her from being happy, and so she does something wrong - extremely wrong - in order to ensure Madoka's happiness. The resolution is not neat or tidy.
It was mentioned in the earlier season that Sayaka is the only magical girl who dies in every single timeline, either by turning into a witch or by overusing her magic. Even Ultimate Madoka couldn't do anything with it since then Kyosuke would land back in hospital. Homuniverse is the first timeline ever in which Sayaka is alive and yet Kyosuke's hand is still healed.
That one thing tells you everything you need to know about the selfish love that Homura used to reshape the universe: Madoka couldn't change Sayaka's outcome without leaving Kyousuke's injury because Sayaka's wish was what made it possible. Homura doesn't just undermine the universe or condemn it to heat death, she negates the meaning of the magical girls' existences. It means that all the magical girls in her new universe gained nothing by becoming magical girls because their wishes have no meaning now.
It's actually pretty doubtful that there are any magical girls in Homura's universe. Kyubey didn't exactly look like he was in any condition to be making contracts, and considering the amount of horrible shit that Homura and her friends went through during the series, it's seriously questionable if she'd even allow him that much freedom in the first place. And while Homura's words imply wraiths are still around, it's not like magical girls are even strictly necessary anymore. Even if Homura isn't doing something like taking the stuff that would form the wraiths and shoving it in Kyubey before it has a chance to spill over and manifest, it's made pretty clear that the Clara Dolls are still around. Each one of them is said to be as strong as a magical girl, there are at least 14 of them, they appear to be able to work in perfect harmony, Homura could probably resurrect any that die (since they're manifestations of her self-loathing and not actual people), and Homura can apparently send them wherever she wants, whenever she wants. Those odds are straight up overkill for anything short of Walpurgisnacht, and anything that strong would still have to contend with the Devil herself. From what little we see, everyone appears to be living happy lives, with whatever problems they had either not existing or not yet manifesting. So it's actually entirely possible that Homura didn't so much render the wishes meaningless as she did make them unnecessary in the first place.
At one point Madoka says it's been a month since Homura transferred in. In the anime Homura says she repeats the same month (and a half) over an over. At the end of the month, Walpurgisnacht appears. In other words, Homura's search for the truth is the equivalent of Walpurgisnacht's appearance.
Wonder how Homura's witch barrier Lotus-Eater Machine was able to alter the memories of Mami and Kyoko? Go back to episode 4. Remember when Madoka gets sucked into Elly's barrier? She gets caught by Elly's familiars and is then altered. Her body changes to resemble the art-style of the barrier. Morever, Madoka is shown images of Mami's death, which suggests Elly is reading her mind. In fact, Madoka only returns to normal when Sayaka attacks Elly. The implication is that anyone "invited" into a witch's barrier is brought under their power. There's no reason to believe witches can't do this to magical girls...but it's easy to see they wouldn't want to since magical girls can fight back. In Rebellion, when Kyubey is giving his explanation we see scenes of Mami and Kyoko doing ordinary things before Homulilly's Clara Doll familiars appear behind them. The Clara Dolls are powerful enough to take on a magical girl, so they must have been able to overpower Mami and Kyoko and bring them to Homulilly's barrier. Once caught by the barrier Mami and Kyoko were "altered" like Madoka was in Elly's barrier...but the alteration was done to their memories.
Some viewers get the impression that Rebellion betrays the point of the original series. Of course it does! With a movie titled Rebellion, how could anyone expect anything less?
Besides, doesn't the resolution of the original series rather betray the theme of the series in the first place? This ending if far more thematically appropriate.
It seems a lot of people were puzzled by the scene when Homura, during her last talk with Sayaka, was showing her hands a lot. She is showing that she doesn't have her contract ring nor the fingernail mark anymore, though she still has her soul gem (or whatever it is now) which could be summoned by Homura, as see in The Stinger. During her talk with Sayaka we're shown in a flash her new earring with a tiny purple jewel on it. It could be she can swap places and make the soul gem less noticeable as an earring.
This makes sense because with Madoka gone, Homura's wish was useless and so she rapidly fell into despair.
Take a good look at the teacup that falls in Homura's new world. Homura isn't dropping it, it's being pushed it out of the way. In fact, she's moving her hand forward, towards where Mami is. Was Homura trying to bother Mami, or was she trying to reach out to her? And then there's the part where she refuses to let her familiars catch Kyoko's apple - as noted below, it's implied the familiars are expressing Homura's true thoughts. Is Homura trying to get Kyoko to waste food, or is she denying her desire for Kyoko's friendship?. One interpretation is that Homura resents them for saving her. Her familiars still represent and play out her self loathing, and she equates herself to the devil because she knows her actions are wrong. She was counting on the two to kill her and cried out against their rescue. Earlier, she confided in Kyoko and flinched over hurting Mami. Her actions are very much intentional, and this is her showing they are no longer on good terms.
Here's something the show doesn't tell you but expects you to figure out yourself. By keeping her from Homura's soul gem, Kyubey's isolation field was blocking Madoka's omniscience. No wonder she couldn't see the movie's outcome. And even after the isolation field is broken, Madoka is still in the form of a human, experiencing time linearly and being unaware of the future.
Madoka wished to erase all witches with her own hands. Now where does Homura grab Madoka?
Wonder why Homura "sent" Madoka to America? Because English was the subject Madoka had the most trouble with.
Pay attention near the end. There's a Pyotr and a bunch of Anthonies in Homura's new world. Obviously they're like Sayaka and Nagisa and are unable to return to the Law of Cycles. This is clearly another part of the Sequel Hook. Heck, during the Homulilly battle we're shown familiars from every single witch seen in the anime... except Walpurgisnacht. And one of the girls who became Walpurgisnacht still sends the elephant afterwards.
Near the end of the movie, Madoka's wearing yellow ribbons. The ribbons are most likely a reference to the first episode. Madoka almost puts on yellow ribbons instead of her signature red ones before her mother tells her that she looks good in red. And since Homura had her red ribbons this time around it seems that she had to settle for them instead. There's even a small echo to what Junko said after Homura gives them back and tells her that they really do look better on her.
She could also be wearing it in reference to a certain other godlike schoolgirl. This may be a nod to an oddly similar plotline. Spoilers for the Haruhi anime: The omnipotent girl's powers were stolen by a normally logical and dependable friend, who became emotionally unstable after an exceedingly long "Groundhog Day" Loop. The latter used the stolen power to construct a more normal and peaceful world for everyone, even though she knows it probably won't last. Is that the plot of Rebellion, or Disappearance? The pre-movie ending of Madoka Magica is somewhat like the "Haruhi's world" ending of Disappearance, while Rebellion takes the "Yuki's world" and The Vanishing of Nagato Yuki-chan route.
The ribbons could also symbolize Madoka's life as a regular girl (pink eyes, pink ribbons) and as Ultimate Madoka (yellow eyes, yellow ribbons). At the end of the series, she gives the pink ones to Homura, symbolizing that she's giving up that life to be the Law of Cycles. Homura wearing them symbolizes how she's living in Madoka's place. At the end of Rebellion, she's wearing the yellow ones initially, but they fall out when she almost remembers and Homura puts the pink ones in her hair instead. Homura is basically giving her her life back.
During Madoka and Homura's conversation in the field of flowers, just before Homura turned into a witch, we can see that the states of the flowers practically summed up Homura's entire journey. Why? Because they are manifestations of Homura's psych, and it was at that point that the idea of becoming The Devil first came to her mind, along with the determination to make Madoka happy. The idea only got reinforced after she had become a witch. "No matter what sin I commit and what form I take, it's all right as long you are near me". This is the moment when Homura finally lose it and breaks down. And this is the moment in which Homura decide she will turn into Devil.
Sayaka being an angel and summoning Oktavia references an ending of The Little Mermaid, where the mermaid becomes an air spirit and gets to go into heaven by doing good deeds. Notably Sayaka is working with the childlike Nagisa; the ending of The Little Mermaid indicated the behavior of children affected the amount of time the mermaid had to work to get into heaven.
The classmates having a face in Homulilly's barrier during the redux of the Nakazawa scene might be weird, given that they are latter seen without a face like the rest of the fake city inhabitants. The reason? At the beginning of the movie, Homura isn't suspecting the masquerade yet, once she start having doubts, the first cracks in the illusion appears with the burned out face of the fake inhabitants. That scene is a subtle hint that the barrier is reacting to Homura's state of mind, foreshadowing that she's the witch who created the barrier.
Of course Homura's soul gem changes shape: it's a crown. Specifically, it's the king's crown as portrayed in chess symbols; meanwhile, the ordinary soul gem does resemble a pawn somewhat. Thus, it's perfectly fitting for someone stepping up to become the Princess of Darkness.Why does it do that? Because nothing, even Kyubey, can undo a wish already granted. If Homura's soul gem really had hatched into a grief seed, even the isolation field wouldn't have prevented Ultimate Madoka from reaching her because her wish was to defeat all witches before they're born, period. However, in the new universe, Homura is her same Bad Ass self she was, even though without a Madoka to protect, she has no reason to make the contract, so what did she wish for? She didn't get one. Her contract was part of the old universe and it carried over, only her powers changed to reflect her new purpose. On top of that, her magical potential would be just as strong as Madoka's, for the same reason. In other words, her soul gem evolves into a crown and she conquers Kyubey because she granted her own fucking wish."
Kyoko isn't seen using her Rosso Fantasma technique in the movie, even though she's kinder and friendlier, and doesn't show traces of her old sour-natured and cynical personality, the reason is that in the pre-Ultimate Madoka universe, Kyoko lost that power when her whole family died, years before Homura contracted and began her time loops to save Madoka, so she doesn't know that Kyoko has that power. So Homulily's barrier couldn't include the knowledge of this power when it altered Kyoko's memories, explaining why she still couldn't use it : she literally forgot that she have that power!
Homura usurping Madoka's rule makes a whole lot of sense when you reflect upon her wish. She wished, in its barest bones, was that she'd be Madoka's protector instead of the other way around. Another way of looking at that wish is that she wished to switch roles. It also explains why Madoka is the transfer student instead of Homura.
The Exact Words of Homura's wish make her rewriting Madoka's universe much less of an Ass Pull when thought over from this angle. Sure, Madoka gained godlike powers due to the constant timelines focused on her, but the wish was still made in a timeline Homura created to redo their meeting...Conversely, Madoka's witch possessed the capability to absorb all life within its barrier. By stopping her from purifying her soul gem, Homura essentially does the same thing.
To add more Poor Communication Kills points to the flower bed scene: Homura is telling to an amnesiac Madoka that she had a dream about Madoka leaving forever, to a far away place, and that she, Homura, wasn't able to see her anymore. Madoka of course felt bad because she would never do something to make her that sad...but Homura didn't tell her that she did it "in the dream" because it was a necessary thing Madoka needed to do because it would save a lot of people. Maybe Homura unconsciously kept that vital information from Madoka, because she wanted this Madoka, either an illusion or a fake, to sympathize with her and say that she would never leave her, forsaking the world's safety for Madoka's happiness.
In Homura's despair sequence, after she fails in saving Madoka from falling down the chair and explodes into pink milkshake, some viewers may find the creepy Moemura-looking things that look down at an angsty and shocked Homura weird and unnecessary. This is actually a nice metaphor: failing to save Madoka from sacrificing herself, she can't forgive herself. That's why her creepy doubles look down on her: she's accusing herself.
At the beginning of the movie, after Homura's brief soliloquy about Magical Girls and their endless fight, her soul gem falls into a open window that symbolizes her potential future salvation by the Law of Cycles, as well-demonstrated by an illustration that came bundled with the OST. At the end we see the same window, closed this time. The window is the way to the Law of Cycles (Madoka), but Homura has kidnapped her and stolen her powers; the Law of Cycles is inaccessible now. Note, however, that the window is not locked or barred shut. It's held together by the very same ribbon that, despite its apparent fragility, symbolizes an unspeakable bond of friendship. This implies that Madoka may recover her powers at any time - but to do so, she needs to renounce Homura's friendship forever, making her situation somewhere between "hostage of her own kindness" and "playing along willingly for Homura's sake".
The reason why the Holy Quintet feeds the Nightmare while singing a lullaby-like song, it's because, normally, you have bad dreams if you go to sleep with a empty stomach.
The "Gott ist tott" scene. The original quote says "God is dead, and we have killed him" referring that, if there's a God, humanity has taken away his purpose with science. Homura is angry that the witch that created the barrier is making null Madoka's sacrifice for the Magical Girls' sake for making a world where their fight has no actual purpose. The Clara dolls, the witch's familiars shout that God is dead because their world has taken Madoka's purpose.
An interpretation of the full quote of "God is dead, and we have killed him. Yet his shadow still looms." is that humans didn't take his purpose, they took his power to fulfill that purpose and had nothing to fill the void leads to an interesting bit of alternate interpretation and possible foreshadowing for future continuation.
Take a good look at everyone's transformation sequences. Almost everyone has runes in them somewhere: Mami, Kyoko, and Sayaka's names, Homura's cryptic messages, and Nagisa's magical girl recipe. Who is the only one without any runes in her sequence? Madoka.
Another one from the transformation: Everyone's music style fits their original personality from the series, except Sayaka's, who switched from classical to break dance. Why? Well she did say that without Kamijou, she wouldn't have been interested in classical music at all... since she retains her original memories, this might be another sign (apart from the ruined moment with Kyoko) that she has moved on from him.
When Homura kidnaps Madoka, we see her split from her Goddess form. The Law of Cycles still exists in the world because Madoka's wish to defeat all witches before they're born still stands, it's just that in Homura's world, there are no witches. So what does that leave? Madoka, a goddess, in human, mortal form. Madoka's wish made her God, Homura's wish made her the Devil... and now Madoka, living in Homura's new world and possibly destined to become Homura's enemy, is Christ.
Akuma Homura tells Kyubey that the Incubators are necessary in her new world because something still has to be done with the curses. Then we see him curled up and traumatized, and we know that since he "eats" grief seeds and cubes, he can absorb curse energy. Homura is forcing him to absorb the grief of her new world in order to keep it a happy place.
Homura becoming what is essentially the devil using The Power of Love makes a huge amount of sense when you consider that she basically turned herself into Madoka's opposite. As Madoka became the embodiment of hope because she loved everyone and wanted to make them happy, Homura became the embodiment of love for one's self, prioritizing one's own happiness over everything else. This can also explain why she can only seal Madoka's powers and not fully remove them from Madoka herself. As long as she can keep Madoka's selflessness in check, she can prevent Madoka from accessing her Goddess powers.
There are a lot of instances where fire, or anything alluding to fire, is shown in the movie because the name "Homura" means "flame."Homura also calls herself a demon after taking Madoka's powers, which is quite fitting because demons are mostly associated with fire, or to be more precise, burning Hell.
Even more meaningfully it can also be written as "heart on fire", "village protector", or "stride approaching happiness".
Kyoko is such a Flat Character because everything is happening in Homura's soul gem. Homura didn't interact with Kyoko enough to know there's more about Kyoko than her brash personality, Big Eater tendencies, her fondess to Sayaka being big enough to die for her so that's all the personal tracts she could give her in her witch barrier. This would also explain why to Homura, Kyoko's character seems strange.
An alternate explanation: Homura seemed to alter their memories so that everything was ideal to each of them. It just had the most noticeable effect on Kyoko. Mami was already a kind mentor, so she remained essentially the same. Madoka had all the psychological torment she went through erased, so she was her original, naive self. And Sayaka wasn't changed at all by the barrier, since her memories weren't altered. Kyoko, however, became a much nicer person in such an ideal world, because her character had been shaped by the terrible world she lived in. She acts so much nicer in the movie because her ruthlessness was rooted in the way the world worked. She likely remembers splitting with Mami on better terms(since she was able to just "call her up" and tell her she needed backup in Mitakihara), and would have had no reason to conflict with Sayaka. Having the others as her friends makes her a nicer person.
Homura's actions in the end meant she was making just as big a sacrifice with just as big a consequence as Madoka did in the anime. Kyubey got what he wanted: he was able to observe the Law of Cycles and could see exactly how Madoka appeared. As long as he keeps making contracts, he'll have infinite opportunities to experiment with ways around it, which means that the chances of Madoka being destroyed, sealed, or otherwise manipulated jumps to 100%. And that would indeed be the case, if Homura hadn't slapped him down so hard he left cracks in the pavement.
Sayaka says she sympathizes with the witch that created the barrier all of them are trapped in because as a former witch, she knows what it is like to want something so badly that a person falls into despair when he or she fails to attain it. This also foreshadows the fact that she knows that it was Homura who was making the barrier, since out of all of them, she never really got what she wanted, despite being the most dedicated to Madoka's cause.
On the possible answer to the question of why the incubators would choose Homura over other magical girls as their lab rat for their isolation field, one could theorize that since they are already operating in a system bound by the Law of Cycles, so anything made within the system, such as Magical Girl contracts and soul gems, would not be a good specimen for their experiment. They probably theorized that Homura, whose magical girl powers did not come from the current system and possesses knowledge of a system they had not known, is somehow connected to the "old" system.
When Homura and Kyoko decided to go to Kazamino city, the reason they cannot get out of Mitakihara city is because Homura doesn't know what Kazamino city looks like, most likely because she has never been there. This also explains why the people have strange looking faces once she begins to uncover more of the truth, aside from the people she knows well, everyone is a stranger to her.
From a logical standpoint, the incubators' plan of trying to control the Law of Cycles fits perfectly well with their characters as purely logical beings. Their quest for finding more efficient ways of collecting energy mirrors how humans are constantly searching for more efficient energy sources.
Think about why Mami suddenly recalls the wraiths. It's Homura's barrier. Mami remembers the wraiths because Homura wants her to remember.
Sayaka has the ability to summon Oktavia, and the familiars of all the defeated witches also participate in the final battle, because of the way the Law of Cycles works. Madoka defeats all the witches before they're born so they don't exist, so what are they even doing there in the first place? Because witches still do exist, they're just never released into the real world. When they become part of the Law of Cycles, their witch becomes their Superpowered Evil Side, just without the "evil" part.
Homura's power to create the universe again is fueled by love. Remember that strong emotions are the power source for the magic they give to magical girls, and that hope and despair are considered opposing elements. Madoka's wish created a world out of hope and destroyed a world with despair. Homura's world is the product of Incubator magic, and she doesn't have a loophole like Madoka does. That's why she's hinted to have turned suicidal in the end: she gave everyone else all their hopes and dreams back and had to shoulder all that negative energy herself, but she's still the girl who relived an entire month and a half, for about a hundred loops, for one single friend and wouldn't hesitate to shoulder such a burden for Madoka's sake.
The Stinger shows Kyubey in Homura's new world, looking battered, bruised, and with its eyes glazed as if it has been, for the lack of a better term, Mind Raped. Remember his words from the series? Amongst his people, emotions are considered a mental illness... and it was just exposed to a love powerful enough (and desperate enough) to usurp God and recreate the universe. That must be the Incubator equivalent of a human getting a good look at the face of Azathoth.
Madoka promised to reunite with Homura again at the end of the series. Homura's head was "planted" with that promise, but Kyubey's interference made her break it and thus Spider Lilies bloomed because the innocent and trusting part of Homura, the Homura that became friend with Madoka would never meet her again.
On the background music, you can still hear parts (albeit slightly modified to fit the feeling of the scene) of the "Mada dame yo" song. Why? We can later see Homura lying on that weird Kyubey table as if she was sleeping. Not only that but the song says the "dream isn't over yet", and that "I wonder what color the morning will be". Of course! The movie isn't over yet and there's still much to see, and in the end, no one really knew what'd happen in the ending.
Adding on to this, "I wonder what color the morning will be" can, aside from commenting on the general surprise of the ending, be a direct reference to a new color, previously unknown to Incubators and magical girls, appearing inside her soul gem.
Just before she turns into a demon, Homura puts her soul gem in her mouth, bites down on it, and breaks it...like a nutcracker. What is Homulilly's title again?
During Homura and Madoka's conversation in the flower field, the daisies transform into dandelions. Considering that you could blow on a dandelion to make a wish...
More Biblical parallels: Once Madoka's memories are erased, she basically becomes a Christ figure (and the pink milkshake scene doesn't hurt, either): a part of God in human form. What does this mean for her? In the series, she didn't know what would happen to her once she made her wish, and she didn't care. If she wants to become Ultimate Madoka again, she has to regain her memories, and consciously choose to sacrifice her mortal self... which also means rejecting Homura.
Hitomi becoming a Victim of the Week is not a coincidence. The time frame of when it happened falls slightly in place of when she became a victim in the anime's time frame. Afterwards, we see Kyoko in her Jerk Ass personality (which is reflected during the bus scene) and the Knight of Cerebus emerges (though it's not Kyoko.), thus leading to a series of tragedies and fights that end in the rise of a new goddess who forever changed the system.
It always bothered me that Homura was able to stave off despair for as long as she could, because even though it was the same fourty-five days over and over, for her, it was still years of being a magical girl with no end in sight; she should have run out of steam ages ago. But then I realized: Homura wanted to save Madoka, and that's all. It's not until she starts to think that it's impossible to save her that her soul gem starts to darken. When Homura tells Kyubey she never wished for the happiness of being with Madoka in magical girl Valhalla, she's telling the absolute truth: in order to keep from falling to despair, she had to stop hoping for anything but exactly what she set out to do in the first place. She can't be let down by a hope she never had. When she says she doesn't care what happens to her as long as it stops Kyubey from doing whatever he wants, she means it.
While we're drawing comparisons between the two, it could be argued that Homura actually ended up nastier than Kyubey by the end. Homura doesn't just not understand Madoka's selfless wish, she outright rejects it, and then takes her power for herself to remake the world to suit her own tastes. People may be legitimately happy in this new world - Madoka included - but with the Incubators under Homura's heel and her constant erasing of people's memories just to maintain Madoka's happiness, which makes Homura happy, it's clear that this new world is meant to make herself happy too, perhaps moreso than Madoka. Worst of all is that she knows she's Jumped Off The Slippery Slope and she's entirely okay with it as long as she believes Madoka is alright.
There's also the fact that Kyubey is physically incapable (so long as he's sane) of feeling or understanding emotions, so can't really be expected to know better. Homura the human, on the other hand, should realize what she's doing—and she probably does—but that doesn't stop her from doing it anyway, because it's what she wants. Which is a... less good motivation than "preventing the destruction of the entire universe".
Kyubey is more villainous than it was in the series, and more openly disdainful of humanity. There are two possible explanations for this: 1) it's been flanderized, and 2) its psyche has begun to crack- and developed emotion. It's possible that Kyubey was already going insane, and Homura's alterations were just the tipping point.
Homura's power is time, and what does she do at the end? Place Madoka back in the flow of time by rendering her mortal.
Homura becomes the Devil, and she slaps down Kyubey with such outrageous pimpness that all he can do is curl up in a ball and stare blankly into nothing, with who-knows-what going on in his fuzzy little fucked-up head. And how, exactly, did they get into such a position for this to be the case? The Incubators had a system that would serve their needs just fine, but the allure of the witch system made them investigate this Kaname Madoka phenomenon in the hopes of making it happen. In other words: they were overcome with Greed. Knowing that the Devil is a fallen Angel, who else is fit to have absolute rule over someone who's fallen to such a grave and deadly sin?
In the series, Sayaka is shown to have awful technique and little to no battlefield awareness. She simply slashes around and only survives because her healing magic means she can take more hits than most magical girls. In this universe, she is shown to be much more competent in how she wields her swords. She's more precise in her strikes and doesn't miss a beat when it comes to a fight. In her confrontation with Homura after the Homura vs. Mami battle, how does she stop Homura from stopping time? She first off has the foresight to predict what Homura was about to do, the reaction time to stop her, and she does so by employing a fencing lunge which is used to quickly close distance between one's self and an opponent. Notice Sayaka's legs right after she clogs Homura's gears. She's poised perfectly, legs bent and sword arm extended, and this form combined with her reaction time and foresight is about as far from her series' self as she can be.
Homura's sand timer tells you everything you need to know about the plot. She shouldn't have it, and we see in the real world that she doesn't. She has it in her labyrinth-dream world because, as she says, she was slowly forgetting Madoka to the point that it was as if she'd just made the whole thing up. She has a bow and arrow in the new universe to reflect her resolve to remember Madoka, but since her despair stems from the failure of that resolve, she manifests herself with her sand timer: the thing that made it possible for her to search for a way to save Madoka over the course of a hundred timelines. Heartbreakingly, that never dawns on her until Madoka appears and reaches out for her again. How could she have her sand timer if Madoka was never real? The fact that she's so consumed by her emotions that she never questions it informs her decision to take hold of the universe at the end; she's too powerful and too driven to stop and think about what she's doing, so all she can do is strive toward a single goal with all her might. And oh, ye gods, is she a mighty, mighty goddess.
The reason why Sayaka could remember Homura's actions while Nagisa didn't. In a Blink-and-You-Miss-It moment, Sayaka is quickly showed again while Homura's soul gem's corruption spreads all over the universe, implying that, somehow she got out of her grasp and fled. This is forshadowed in the secene when she almost summoned Oktavia and Homura pointed up how Sayaka has gotten better at running away.
Houmura is a Devil in many, many ways beyond the whole Fallen Hero gig. For one, she's defined by obsessive love fed at least partially by a sense of betrayal; Izanami, estranged wife of Izangi and Japanese goddess of the underworld. For another she tricked a god in order to bring happiness to humans (actually two divine figures; Madoka and Kyubey); Prometheus, the Titan who stole fire and bound his cousin Zeus into only taking the inedible bits of a sacrifice, and got to be gnawed on by a Stymphalian Bird for a few eons as punishment. Third, her tricks bring about a final battle and the rebirth of the world into a hopefully better form; Loki of the Norse Pantheon, whose murder of Balder and later impersonation of a giantess started up Ragnarok. Fourth, she creates and rules over a world where people labor in cheerful ignorance of reality in the belief that's what they want, mimicking the actual God in the process; The Demiurge, lord of the visible and physical worlds in Gnosticism. Finally, said obsessive love can be said to be a testament to virtues gone awry and a complete loss of restraint, and her ability to implement it showing her resourcefulness and raw power; the Tarot Devil. Really, she doesn't exactly have a small pedigree.
Several versions of the Buddha story include the character Channa, a royal charioteer. At the King's orders, he tried to prevent the Buddha from learning about the existence of suffering (death, age, illness, etc). In the end, Channa failed, and the Buddha left his home and became spiritually enlightened note discarding his previous, mortal, identity in the process. If we consider Puella's other Buddhist themes, Channa's story becomes yet another indication that Homura's utopian world cannot last, and Madoka too is destined to 'leave home', regardless of what Homura does.
Madoka had enough power to make huge changes in the world, but instead, she opted only to make one change, and became the principle that destroys witches. She respected the contributions of magical girls enough to still let them make contracts, which inevitably assured their deaths. In other words, Madoka preserved their right to want something bad enough to die for it, aka, she gives them free will. That's part of what makes Homura's crimes so terrible: she made a world where everyone has what they've always wanted, but she's taken away their free will in order to impose her own. It's the difference between selfless love and selfish love.
The stinger from the end of the TV series, where Homura confronts a bunch of wraiths in a weird desert and sprouts her weird witch wings? Those wings are immediately followed by a network of strings made of light. It's the isolation field being put into place. In order to preserve the integrity of the experiment, Kyubey would've needed to take Homura away from all immediate outside influences so that he could be sure that no one got into it accidentally or caused any damage to Homura's physical body while she was under observation. At the end of the movie, the entire remaining cast ends up in that exact same desert.
Sayaka's transformation music uses her old theme, "Decretum", but notably in a modern style and with modern dance. Why, when she presumably became a magical girl by healing Kyosuke here too and her earlier affinity with classical music was due to Kamijou? (She herself said, "I wouldn't even be interested in this kinda music if not for you.") Because she is over him, as evidenced by her being understanding and full of sympathy while helping Hitomi, who is currently going out with him... Especially since this is the Sayaka we know, the Sayaka who attained peace thanks to being able to listen to Kamijou play at a contest.
Notice the words Sayaka uses to describe the color of the corruption in Homura's Soul Gem: Desire and Insasiability, and Nagisa calls it "a color worse than curses". This is a good contrast between Madoka's selfless, agape love and Homura's selfish desire of protecting Madoka, that she justifies saying it's her love towards her and how such devotion is very unhealthy.
Fridge Sadness. In all of the flashbacks during Kyubey's exposition about Homura's barrier, all girls are seen wearing casual clothes and doing things together and when Homura is seen with them, they're all in uniforms. Homura doesn't known about lounging. Her early life was first being in the hospital for her heart condition; then in her first day of school she met magical girls who became her friends but were busy fighting. When she got to became a magical girl herself, her time got reduced to repeating a month of fighting over and over, with some little school life in it. And when the cycle was broken, she just focused on fighting wraiths instead of witches. Homura's own focus on anxious schooling and desperate fighting were so strong in her subconcious that it was the way her barrier portrait her; and having such a peaceful life was so alien to her that it was the thing that made her realize something was wrong. BECAUSE THERE'S NO WAY HOMURA CAN BE HAPPY!
The TV behind Homura, when Mami is confronting her over attacking Bebe, shows teeth falling from the upper jaw of a mouth. It's the Nutcracker Witch's mouth, obviously, but "teeth falling out" is one of the most common types of all nightmares: anxiety, low-self-esteem, fear of major changes, and broken promises. It ties into her suffering as a magical girl in general, but in particular, a nutcracker cracks nuts by biting them in half, while Homulilly has no upper jaw and her teeth serve as mounts for her familiars. In other words, she can't perform her sole function (cracking nuts/saving Madoka) because, in becoming the thing that serves that function (a witch/a magical girl), she made herself incapable of actually performing it (missing the top of half of her head/wishing to go back in time).
Mami's entire presence in the movie is chock-full of fridge brilliance. She gets relatively little screentime outside of the epic fight scenes, but they pack a lot of character into the details:
Mami and Bebe = Mommy and Baby, d'aww.
Mami being Crazy-Prepared in the battle against Homura makes sense because she's the team veteran, but Homura has technically been a magical girl for roughly twelve years and has solo-killed more witches than Mami could possibly ever encounter, due to her time-looping. Homura can't beat Mami because Homura still thinks of her as an older, more experienced mentor figure. Mami deflects all of Homura's shots because Homura always fires first (in other words, Mami is only reacting to Homura's attacks, not attacking herself), and when Mami breaks out the red-lock ribbons, it's because Homura didn't have the stomach to shatter her Soul Gem. She didn't actually want to hurt Mami, she just didn't think it through before resorting to violence.
Most likely coincidence, but fun anyway: purple and yellow are complementary colors.
Mami knows Homura didn't want to kill her because she didn't shoot her Soul Gem out. In the anime, the only time Mami ever found out what a Soul Gem is, she committed murder-suicide. In the new timeline, Kyubey has no reason to hide the truth about Soul Gems, so of course she'd know about it. It's another clue that something isn't right with the world, but Homura doesn't pick up on it.
Part of Sayaka's transformation sequences sees her charging into and merging with her magical girl form from a running start, almost as if she's chasing her magical girl form. Sayaka was the one in the show who was always trying to be a hero, or in other words chasing an ideal that she thought her magical girl form represented.
Homura's familiars have splendid names like "Arrogance," "Sadsack," "Liar," "Coldheartedness," "Selfishness," "Badmouther," "Dunce," "Jealousy," "Lazybones," "Vanity," "Cowardice," "Fool," "Bias," and "Obstinance." And the last familiar? Its name is "Love," and it has yet to arrive. One can naturally conclude why Homura would want to surround herself with representations of her perceived negative qualities but not one of love.
On the other hand, the eventual arrival of "Love" may actually point towards an optimistic ending in the franchise, and that hope still exists for Homura, preserving the original theme of the series.
Alternatively Love is Homura herself. This seems to be supported by the clothes "Love" wears is identical (except for being bald) to the one Homura wears prior Homulilly's resurrection. So either "Love" is marking redemption, or "Love" already died and the so-called arrival will never arrive.
The guidebook explicitly called Love "A Devil". It's probably safe to assume that Homura's Love herself.
Perhaps the reason that Love hasn't appeared is due to the factor that the Clara Dolls are representations of what she thinks of herself. She clearly doesn't love herself and as such the corresponding familiar wouldn't appear. But going with the above suggestion, Homura being Love herself could be fitting, given the possibility of it pointing to hope for Homura. Afterall, love is supposed to begin with the self.
Homura's barrier has been extended to cover the entire universe. Considering what its inside is like, that's not a good news for anyone who lives in the universe... which is everyone. What if Homura's Nightmares begin to plague the entire cosmos? What if the Nightmares have become exacerbated due to Homura's extreme guilt? What if the Nightmare grow proportionally to Homura's guilt, which will eventually become too monumental for anyone to deal with, magical girls or no?
Actually, the new Homuniverse might be a good solution to the heat death problem. Both the old system with witches and Madoka's weren't very efficient. In both systems, the average magical girls on normal people ratio was about 2 on several thousands. The average lifespan of a magical girls could be anything between 1 month and 5 or 6 years after making the contract. In the old system, although the energy was harvested in both stages of witch and magical girl, most energy was harvested in the transformation between the 2 stages in which entropy was at its maximum. In Madoka's system, energy was only harvested in the magical girl stage, making it even less efficient. However, in Homura system, nightmares can come from every single person in the population of 7 billion and counting. With a little bit of despair from everyone, the collective energy would be HUGE, even with the generous way nightmares cleanse the soul gems. In addition to that, the energy from the magical girls and possible witches who would most definitely exist, seeing there isn't any Godoka there to cleanse the girls' soul gems, wouldn't hurt either. To put it bluntly, the old system was akin to the way a farmer from the Middle Age would raise cattle, the Madoka system was the more humane way that animal rights activists prefer at the cost of efficiency, the new Homura system was the way an industrialist would raise cattle: more humane than the old system but still crueler than Madoka's system, but above all, it treasures efficiency at the obvious cost of " environmental pollution" (i.e: the possible destruction of civilization). As Sir Terry Pratchett had put it: "... you had to think differently these days. Not big, but wide. With five billion people in the world you couldn't pick the buggers off one by one any more; you had to spread your effort." And if the destruction the nightmares cause goes a bit out of hand, well, that's neither Homura nor Kyubey's problem to worry about. Homura could always wave it away if Madoka's in danger, seeing as she IS the absolute dictator of the new universe.
All this is assuming the new universe isn't simply immune to the laws of physics to begin with, because magic actively protects it from all possible harm. It also allows ordinary sentient creatures and those created magically to coexist freely, which is, at least in theory, a good thing given that familiars have been demonstrating numerous sympathetic qualities in the movie. The only problem is that Homura is this world's absolute master and thus it may change in accordance with her mental state, without her explicit volition. Considering said state's fragility, the prospect might be troubling.
Take a look at the scene where Sayaka and Homura are talking in Homura's new world. Homura is acting every bit like a villain, but pay attention to what the familiars are doing. Not only do they throw tomatoes at her, but before that there's a scene where the familiars are jumping off a ledge with empty shoes on it. In Japan this is a metaphor for suicide. It's suggests that Homura is just putting on another persona, and that she's really in her own Self-Inflicted Hell.
It's also assuming that this world even has nightmares or wraiths or whatever. Given what happened to Kyubey, they might not exist at all.
And just in case that wasn't obvious enough, in The Stinger she willingly falls off a cliff.
This is also the only time where she seems truly happy. Make of that what you will.
The Clara Dolls are Homulilly's familiars and their role is playing mourners for the witch's execution. Homura is an orphan, has no other friends aside the Magical Girls and she's convinced that they will be more focused in killing her than crying for her death. She's believes that she will be Dying Alone and nobody will mourn or lament her death, so she created the Clara Dolls to give to herself the illusion of someone sad for her.
What's worse is, they won't even do that. The tears they shed are fake, as evidenced by their permanent Slasher Smile expression, and in Akuma Homura's new world their job is now to mock their mistress forever. Really, there's something very wrong with this girl.
Nagisa running around and frolicking in Homura's new world is adorable, until it hits you: it's not unreasonable to assume that considering her nature she, like Sayaka, remembers what had just transpired. But unlike Sayaka, Nagisa is over the moon. Does that mean she's okay with what Homura did...?
It's more likely that Homura already altered Nagisa's memory, as she did to Sayaka; unlike Sayaka, Homura has no real connection with Nagisa, so she'd have no reason to converse with her the way she did with Sayaka before wiping her memories.
Still, she seemed WAY too happy considering the circumstances. This wasn't her just skipping all carefree down the road on her way to school, she was out-and-out cavorting: running full speed with her arms outstretched, spinning around, dancing and laughing her head off. And then she becomes pretty much 'normal' again when she meets up with who I assume are her classmates. She was also in the 'wine world' alone with Sayaka and Homura: she could probably see it.
It's easy to forget that Nagisa is the Charlotte of the post-Madoka wraith world. Since Kyubey would have contracted with her without needing her to become a witch, her wish probably didn't tragically and since she's alive now, she never used up her magic. She isn't sad because she doesn't have anything to be sad about, and all the things that would have ruined it for her have been edited out of her memory.
If the Law of Cycles is now broken thanks to Homura, what happens to the magical girls who were taken to Magical Girl Valhalla? They're essentially trapped there now, since only Madoka has the power to send agents back to Earth. Consequently, no Magical Girl will be able to go there now as well, and as Homura explicitly states, those who have returned from that place, like Sayaka and Nagisa, can never go back. It is also implied that Homura essentially created a universe-wide Lotus-Eater Machine, since she's able to alter the memories of everybody including Sayaka, Nagisa, and especially, Madoka.
There's new information on the Puella Magi wiki about Homura's seemingly decorative earring: it's the place where Madoka's powers are sealed, and the thing actually acts as a communication trinket between Homura and her familiars, but what makes it scary it's that it's partially sentient. But it doesn't end there. That tiny jewel dingling from its tail? It's Madoka's soul gem and its eye is Homura's.
If you made it this far, you know this means Madoka will start decomposing and die if she's ever away from Humora for an extended period of time.
The whole final battle is, unknown to everyone but Homura and Kyubey, a last-ditch effort to keep Kyubey from learning more about and subsequently enslaving Madoka via Heroic Sacrifice. Other than losing a few expendable bodies when containment fails, it's an unqualified victory for the Incubators until Homura makes her final play. Her actions may have subverted Madoka's sacrifice, but not doing it would have led to the benefits being completely undone.
On top of that, much like in the original universe, their efforts are ultimately doomed to fail without Homura interfering with Madoka. Think about it: what, exactly, would keep the incubators from doing the exact same thing to other magical girls until the Ultimate Madoka squad screwed up and let her get captured? The Law of the Cycles was doomed to be undone by the incubators from the moment Homura foolishly told Kyubey about the old system. As selfish as it was, Homura's actions at the end of the plot were likely the only way to truly save Madoka.
There's a couple of different ways to interpret the ending, but if you take it as Homura re-ordering the universe so that magical girls get wishes but don't have to fight because Homura is forcing the Incubators to absorb the equivalent despair this raises some disturbing possibilities about Kyubey. If Homura is forcing the Incubators to absorb despair, does that mean they'll be forced to develop emotions? If they do... will they be able to make wishes?
How much of the truth about Kyubey does Homura actually know? Obviously she knows what happens to magical girls and witches and the balance of hope and despair, but what about entropy and the heat death of the universe? Kyubey only told Madoka about that in private, and Homura has no real reason to ask. If she has a single tragic flaw, it's that she's constantly throwing her whole being into a single specific goal without all the facts. What if she doesn't know why the Incubators want to collect the energy of human emotions? What if she knows, but doesn't understand thermodynamics enough to really get it? What if she just plain has no idea? It would mean that she's not selfishly damning the universe just for Madoka out of greed or spite, she's doing it out of ignorance, and she's already removed or cowed almost everyone who could correct her...
The question is, what does he really know? His entire plan is to harvest the power of emotion, and he doesn't understand emotion. He knows enough to manipulate girls into becoming magical girls and ultimately witches, but is so inconsistent it seems like he figured it out by trial and error. Seriously, he's been doing this for centuries and he doesn't know what love is. For that matter it would be completely insane to trust anything he says about his motivations, speaking in half truths and purposely omitting crucial details is his entire schtick.
How much does it matter? Homura's running the show now. Kyubey's understanding is practically a moot point now.
It matters a lot. Homura's running the show, but we don't know what's going on in his head now, except that he's probably traumatized. The whole point of seeking a race of creatures where each has its own emotions was to harvest them for grief because, although the Incubators don't fully understand emotions themselves, they do know that emotional energy is a potentially limitless power that isn't bound by the laws of thermodynamics. If that means Kyubey, being forced to endure whatever Homura is doing to him in a way that teaches him what it means to feel (and since emotions are a mental illness for Incubators, that would mean Homura is torturing him into insanity), he's still the only character who knows how Incubator technology actually works. Madoka and Homura use it to ends he can't fully grasp in the moment, but only he can make the contract. And if he has emotions, if he's willing to sign himself away for the sake of the universe, what's stopping him from doing exactly that? Considering that no less than four entire universes and a hundred timeliness have been created and destroyed solely because Kyubey came to earth, his karmic destiny is greater than the karmic destiny of literally all other magical girls combined. There is nothing in the universe that could be more frightening than a Kyubey who is capable of making a wish.
So, the whole point of this was to isolate Homura's soul gem within a barrier so that the Incubators could have proof that "The Entity Called Madoka Kaname" exists, with the knowledge that if it exists, it can one day be manipulated. But here's the kicker: the Incubators only wanted that because they wanted to bring about the witch system, because it would be more efficient than grief cubes. Madoka knew exactly what Kyubey was doing and divided herself up between three ordinary magical girls, choosing only to show her true form once the isolation field was gone and the Incubators were no better off than they were at the start; with Madoka appearing only within Homura's soul gem, the Incubators would have no way of knowing if she were real, or if she was just a figment of Homura's imagination. Madoka's wish ensured that witches could never come about again, there was no chance of that ever changing. But then Homura jumped the gun and split her off from herself, and it's all downhill from there. So, bottom line? Homura lost her faith.
Homura made a new universe with magic. Thing is, Homura is removed from the hope/despair equation. She does it with love, but it's still Incubator technology, and we know that every application of that technology has its price that the magical girl has to pay no matter who gets the benefit of her wish. And what's the opposite of love, but hate? That's why she's implied to be suicidal, why she cuts off contact with her friends, why she openly transgresses against Madoka just for the sake of protecting her and making everyone happy. She loves Madoka enough to create an entire universe... which is also enough hate to destroy one.
It's stated that after becoming part of the Law of Cycles, Sayaka gained the memories of previous incarnations which explains her knowledge of the witch system and her improved fighting techniques. However, besides turning into a witch in other timelines, its implied that she also remembers being a witch as indicated by her comment about how Homulilly is suffering the most. This would mean that she has memories of attempting to crush Madoka as Oktavia and Kyoko committing a Heroic Sacrifice to take her down. One has to wonder how much guilt she must be carrying.
No one but Madoka and Homura are ever shown to remember the pre-Ultimate Madoka timelines, so it's unlikely that Sayaka can remember trying to kill Madoka as Oktavia or Kyoko's Heroic Sacrifice. However, her comments about Homulilly suggest that Madoka's trip into Homura's soul gem is more complicated than usual due to the isolation field, but not actually different. When Madoka comes to fetch a magical girl home to Valhalla, what she's really doing is fighting and defeating the witch inside the soul gem in a super-compressed "I Know You Are in There Somewhere" Fight.
The isolation field itself carries some terrifying implications. Homura's descent into despair begins when she begins to doubt herself, thinking that Madoka was imaginary, right? We don't know when she started thinking that, but we do know that the isolation field itself is something of a prism-like seal around the illusory world inside the soul gem, and that no one can get into it without being drawn in by a witch. Think about that for a second: the Incubators put a seal over Homura's very soul, one that couldn't be breached until she accrued enough despair or used enough magic to turn into a witch in the first place. Homura may have been rendered completely inable of having emotional connections to anyone not in her soul gem. Of course she came to doubt Madoka, she was completely and utterly alone within herself.
During her final dialogue with Sayaka, Homura says something along the lines of "if you continue to act confrontational all the time, even she might come to dislike you." Given the show's almost entirely female cast, the precise identity of "she" is a bit ambiguous. If you assume that Homura's referring to Madoka, it's suggesting the loss of Sayaka's closest friend and the absolute failure of Sayaka's goals. However, if you interpret Homura's threat as referring to Kyoko, that's when Homura's psychological beatdown reaches a new stage of fucked-up. In the context of Sayaka's confession not thirty minutes prior, the implications are curl-up-in-the-corner-hugging-a-pillow inducing. Homura isn't threatening Sayaka physically, she's threatening her relationship with the person she cares most about.
Homulilly's endless funeral procession. Of course there's no peace for her, that's not really what a witch is all about, but Homulilly's awful fate is to simply walk. Forever. Being mocked and disdained by all she passes, never able to make a true end of it. Her hands are shackled to her purpose, but a part of her claws the ground in her wake in a futile attempt to stop herself. Sound familiar? She was fortunate enough to retain her human form the entire time, but essentially, Homura's life as a magical girl was only cosmetically different from her life as a witch.
Homura is clearly in control of her self as a witch. She created her labyrinths to create a better world for her close friends and their close friends and never curses anyone. She later trys to commit suicide by magical girl so she was still in control the whole way. And Sayaka implies this is the case for all witches. In other words the witches have never been mindless monsters. The attempt to save Sayaka didn't work because she already knew who Madoka was and targeted her anyways for her own reasons.
Kyubey's intentions for the Law of the Cycle. His reasoning is that if he can observe it, he can interfere with it, and if he can interfere with it, he can control it. He doesn't realize that the Law of the Cycle is literally the law that the entire universe was built around, he only sees it as a physical law. While that is technically correct, it means he doesn't know that that law can't be broken because he views Madoka as a person, not a principle in human form. So why is that bad? Because he has undeniable proof that Witches still do exist, they just don't manifest in the real world. He originated all this Sufficiently Advanced Technology, all he has to do to keep Madoka out of the equation is adjust the Soul Gem formula so that the witch stays confined inside the Soul Gem and can't get out. Madoka's wish specifically granted her the power to defeat all witches before they're born and she only appears when magical girls are on the brink of despair, if the Incubators simply change it so that witches can't be born at all, then they can just go into the Soul Gems (like we see him do with Homura's) and do whatever they want with the witch trapped inside.
And, possibly worse, that would be an extremely easy thing for Kyubey to sell to magical girls. He'd be able to tell them "Your friend has something truly dangerous growing inside her Soul Gem. If you don't do something to stop it, the Law of the Cycle will kill her!" and be telling the absolute truth.
Homura's most insurmountable hurdle is getting the other magical girls to believe anything she tells them. At least with Walpurgis, her attacks actually landed even if they didn't cause her much damage; the girls never believe anything she tells them, so she just doesn't bother anymore and accepts that she'll have to do everything alone. Now think back to the epic Homura vs Mami battle over Bebe. The first thing Mami does is to tell Homura that she wanted to stay back until she understood what was going on, but had to intervene to protect Bebe, and then just straight-out asks her what she's trying to do. Keep in mind, this is the first time anyone besides Madoka has honestly asked her to explain herself instead of immediately judging her for not being nice. Homura hesitates, but you can see her make the conscious decision to have faith in her friend— while the giant TV display shows a procession of lonely Homuras marching across an empty void— and tells her the truth....and Mami not only doesn't believe her, she not-so-subtly says she thinks Homura's not right in the head (which is true, but not for the reasons Mami thinks). After everything she's been through and all the pain she's in at that moment, Homura took yet another chance on trusting her friend, and yet again, her friend let her down. Homura gets a lot of crap for never explaining herself and always trying to do everything on her own, but the other girls never listen to her. There's no point in asking for help when they repeatedly show her, in multiple timelines, that they will write her off as a liar if she tries. And now, the proper Fridge Horror part: Kyubey is frequently interpreted as a trafficker or child predator. What's the most common reason abuse victims don't report their abuser? They think no one will believe them.
Nagisa gives her reason for coming back as wanting to eat cheese again. Sounds cute and innocent, right? That is, until one recalls that as Bebe she refers to Mami - or at least her Magical Girl form - as "Cheese" twice,note When Charlotte senses Hitomi's Nightmare, she tells Mami to "Turn into cheese!"; and during the Cake Song she looks at Mami and says "Cheese?" and Mami refers to herself as "the cheese" in the Cake Song. Remember what Charlotte did to Mami in the third episode of the original anime? Not so cute and innocent now, is it?
Homura has been cycling through time... a lot. And she looks as young as she ever has. Until she turns into a witch. And then you realize that she's old. Really old. And obviously, she sounds really depressed: sick of cycling over and over just to do one thing, and only after succeeding after countless failures, she has nothing more to do. Maybe Homura gives up on hope just because she's unimaginably tired. She literally can't keep going. After all, nobody is meant to live that long. When you take the falling teeth and severed head literally...
It makes sense that she'd be tired of going over the same month again and again so many times, but even 100 loops of 30 days is still only a little over eight years. At the absolute most, Homura can't be more than about 24 years old.