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Here’s the thing that Homura never admitted to herself, even when she was tearing her crush apart:
Madoka Kaname wasn’t human. Not in the slightest.
And to be entirely accurate, she wasn’t really Madoka Kaname either. Madoka was like an old jacket that was held onto out of fondness, even if the owner had grown too big for it to really be comfortable anymore. The nostalgia of wearing it overrode the actual experience.
The tiny human soul which originally bore Madoka's name had long since been supplanted by something much grander, although it still remained as part of the core. It was similar to an acorn that has produced a towering, ancient oak tree. Technically, what remains of the acorn is still in there somewhere, amongst the roots. But in more practical terms it is simply gone.
The basic fact of the matter is that The Law of Cycles was just that. A law of the universe. Not an entirely natural one either, even if it had now stood firm for all of time. It was a law written by a teenage girl who had set her very soul alight and scrawled over the fabric of reality with the ash.
To be clear, The Law of Cycles still had a soul. Or, more accurately, she had a multitude of souls, and subsumed more with every passing day. The new existence that Madoka had forged for herself was not something that any human could really comprehend. If a human soul was a gem, then The Law of Cycles’ looked like a brilliant rose quartz. Somewhat. Of course, there was no natural object that could truly be used as a comparison for such a thing. It was made of warm hands and a kind smile and inevitability and a very particular kind of mercy. This was the soul of a being who had found the cultivation of corrupted souls to be a cruelty, so she chose to harvest the ripening fruit herself. Scrumping on an incomprehensible scale. The Incubators were basically farmers looking for a solution. And so Homura Akemi became their combined burglar alarm and trap.
The Law of Cycles saw all this and acted anyway. And afterwards, when Homura had stolen her favourite jacket away, she couldn’t quite understand why she had gotten involved so deeply anymore. She had millions of magical girls willing to fight in her name, and plenty of them had lasted longer than the single month Madoka had. Any one of them would have been able to poke a hole in the barrier for her to shoot an arrow through. Homura Akemi wasn’t that important. Right?
Of course, The Law of Cycles was not heartless, no matter how little she understood humanity. She could see a brewing problem when she saw it. And so she made herself a new dress the moment that thought crossed her mind.
This dress was the purest of whites. It clung to the figure of a beautiful woman, and was decorated with flashes of gold. Crystal heels the colour of her soul graced her feet, matching the long and cascading tresses of her hair. The Law of Cycles looked at herself in the mirror and thought that this was the appearance of a goddess. She smiled. It suited her more than that old jacket ever did.
Another point for consideration: although Madoka was never one to display vanity or pride, let alone arrogance, she still wished to become something more. There were plenty of ways to phrase that wish, ways which would have allowed her to create The Law of Cycles without also becoming its vessel. Then again, with the wreckage of so many wishes-gone-wrong around her, Madoka simply hadn't trusted pure magic to understand human empathy by itself. An understandable reason, but still.
In any case, with the creation of her new dress and form, The Law of Cycles had something approaching a proper sense of empathy again. She was still not Madoka Kaname, of course, but that was a problem she was far better equipped to deal with now.
She flew to where the trap lay without a hint of hesitation. It had already been sprung, after all, and even clamped down on the tails of its creators as it did so. The biggest concern now was little more than a petulant child.
Homura Akemi considered herself a goddess, or at the very least a devil. There are words for humans who think like that, but ‘accurate’ is typically not one of them. In reality, Homura Akemi was a hysterical teenager playing dress-up in a goddess’ stolen jacket. If the girl wasn’t mostly mad from grief, and one of hers besides, The Law of Cycles probably would have done something remarkably nasty in retribution.
As it was, she stretched out a single finger. For just a moment, the long, manicured nail which topped it looked more like a witch’s claw. The cheerful pink polish soured and blackened, bubbling and roiling in a poison made from a thousand deadly curses.
There was no more need for subtlety. The barest hint of Kriemhild Gretchen ravaged the Incubators’ cage with a gleeful cackle.
The Law of Cycles strode inside the co-opted labyrinth as if she owned it. From a certain point of view, she did. Magical girls came to reside within her, and their witches became a part of her through Gretchen. Homura had a foot in either world and a stolen fragment of divinity, but that didn’t change the fact that she still ultimately came under The Law of Cycles’ authority. If anything, it made it clearer.
Speaking of the girl she was supposed to love, the half-witch soon found and charged at The Law of Cycles in a blind rage. Trailing behind her came the group of magical girls originally sent to free the girl, as well as the somewhat-lobotomised Madoka.
The Law of Cycles was not typically an angry goddess, but she had just called upon her witch for the first time and was still riding high on the moment of catharsis. So she extended a graceful leg and met her would-be beloved with a spiked heel to the gut. Nails that were still just slightly too sharp drew blood from the follow-up slap to the face.
As Homura went flying, The Law of Cycles took the opportunity to pull the lining of her jacket from where it had been tied awkwardly around the magical girl’s shoulders like a cape. The girl was instantly lesser, but still froze time the moment she recovered and prepared to launch a counterattack.
In response to this, The Law of Cycles drove Homura into the ground with an axe kick. Time quickly took the hint and restarted itself.
“Who— what are you?!” Homura screeched.
The Law of Cycles shot Madoka an extremely unimpressed look.
The hopelessly confused fragment just blinked back at her, too dazed to really understand what was happening. “Oh no, Homura-chan!” she said, her voice just slightly too dull for the words to be truly heartfelt.
The Law of Cycles rolled her eyes, walked over and folded up the rest of her jacket, stuffing the lining back inside and tucking it all away for later.
Homura howled at the sight. Still lying prone on the ground, she pulled out a pistol and fired. At the same time, magical ribbons encircled The Law of Cycles, a sword and spear stabbed at her, and a flurry of bubbles splattered against her face.
The Law of Cycles simply sighed and swallowed the magical girls whole. There. Five souls claimed, including four returnees. Easy. The labyrinth instantly began to collapse around her, Gretchen greedily slurping the grief down into her shadow. She turned on her heel to leave.
A shaky limb reached out and pawed at her shoe. The Law of Cycles paused. She looked down. Even without Madoka in place, she grimaced.
Kyubey was a sorry sight. Its bedraggled fur was ripped and torn, its eyes were dull. Every muscle twitched in pain.
“P-please…h-helllllp…uuuussss...”
The Law of Cycles was uninterested in restoring the Incubators’ sociopathy, which was what Kyubey meant. But she would still help them, because that was who she was. And so she offered them a contract. The opportunity for respite, in exchange for becoming her familiars. Kyubey signed without a second thought, and through it all Incubators were bound to the same terms.
In that moment, the Incubators truly understood mercy, compassion, and forgiveness. They also learned that the simple knowledge of these things would never be enough. They would have to earn it. As one, they wailed.
But in the end, they could hardly complain. They had offered much more twisted deals themselves, and with far crueller intent. Already they no longer felt the pain that Homura had forced on them, and that wasn’t even technically part of the deal. She had offered a chance for respite, not respite in and of itself. Because the guilt remained, and with it the horror, nausea, and heart-rending agony it caused.
“From now on, the Incubators will ensure that the terms and consequences of a contract are explicitly stated and understood,” The Law of Cycles said. Not so much an instruction as an inviolable decree. It wasn't a perfect solution, of course; the wraiths born of the darkness in human hearts would still need to be fought by magical girls. But then, that was life for you.
Kyubey slumped into a boneless heap. “Yes, my Lady,” it said, miserable and relieved all at once.
With that accomplished, The Law of Cycles decided that her business was done, and quickly left before Kyubey could ask her for anything else. Stepping through the hole she had torn in the fake horizon, she emerged onto the familiar streets of Mitakihara. She briefly considered visiting the Kaname family, but in the end she just sequestered herself in what could have been her bedroom and did what she probably should have done long ago. She retailored her jacket.
It was incredibly simple work in the end. Just a few steps closer to divinity here, a piece of wistful make-believe thrown away there. What emerged was a Madoka Kaname who was both more in line with her true self and no less 'human' for it. The Law of Cycles slipped the faux-mortal jacket on, a perfect complement to the divine dress underneath despite the radically different styles. It softened the whole look into something much more approachable. And then—
Madoka Kaname blinked. After a moment of taking stock, the young woman buried her face in her hands and allowed herself to say a quiet curse word or two. Literal aeons as a child, and then her greater self decided to speedrun puberty the moment they lost touch. Yes, she understood the need for it, and yes, she was obviously overdue to grow up at this point, but this was still not how she had wanted to do it!
Madoka gave herself a few quiet minutes to come to terms with it all. She was owed that much, even if she was still just a goddess playing pretend. Then she stood up, marvelled for a second at how easy it was to walk in her new shoes, and hurried into the depths of the Cycle. As she did so, she temporarily shed a few of her apparent years for familiarity’s sake. It was only skin-deep, of course, and that probably wasn’t going to change again any time soon. Still, she had an extremely traumatised sort-of girlfriend to comfort, not to mention their friends; it would be easier for them if she looked like this for the time being. Besides, the whole 'millennia-long age gap' talk should probably wait until she was sure that Homura was actually sane again.