I have a confession to make. I am not a clever guy.
So with that out of the way, does anyone have a good writeup to link me to that goes into what Rebellion was about? Watched it twice but couldn't make much sense of it even if someone held me at gunpoint
(The ending of regular Madoka Magica made sense to me, so got that covered at least).
I don't know how deep you want to go with it, but I'll give you a rough summary of events as I understood them.
At the end of Madoka Magica, Madoka wished to personally mercy kill every magical girl in history just before they witched out. This resulted in history being retconned in a way that Homura was the only one who remembered how things used to work. In the new timeline, Kyubey just knew that when Soul Gems get sufficiently filled with Grief, they spontaneously vanish. This phenomenon is referred to as the Law of Cycles. Homura talked about her experiences in the pre-retcon timeline with Kyubey.
Kyubey was intrigued by the idea of the old witch system and finding out that the Law of Cycles might be a time traveling magical girl, decided that if it was true, they might be able to stop Madoka's actions and go back to the witch system, which had higher energy yield than the new way things were working.
Kyubey's experiment involved trapping Homura inside a supertech isolation field to keep any outside influence out of it while pushing her Soul Gem to the very edge of its limit. The idea was that when Madoka showed up to collect Homura to prevent her from witching out, the Incubators would be able to observe the event and use what they learned to work out a way to put a stop to the Law of Cycles permanently.
Most of the movie is Homura in a quasi-barrier as she's teetering on the edge of witching out. The Incubator isolation field allowed her to draw people into the quasi-barrier as part of how they were handling their observation of the experiment. Since Homura knew Madoka personally, that invitation mechanism was somehow related to them observing Madoka and gathering data on how to stop her.
Kyubey underestimated Madoka's intelligence, again. Madoka played a memory gambit by taking the already dead Sayaka and Nagisa and having them hold on to her memories and powers when the three of them passed into the barrier. This made it harder for Kyubey to figure out exactly how much of their presence was related to the Law of Cycles experiment and how much was Homura summoning up quasi-familiars of her fallen friends.
Over the course of the movie, Homura gradually works out what's happened and where she is. Meanwhile, because Madoka's running a memory gambit, she doesn't know why she decided to become the Law of Cycles in the first place, so Homura and Madoka have a conversation where they talk past eachother that convinces Homura that Madoka isn't really happy being the Law of Cycles.
Homura had been getting by believing that Madoka was happy and safely beyond the Incubators' ability to harm, but the combination of the conversation with the amnesiac Madoka and Kyubey actively trying to fuck with Madoka again caused Homura to snap. She decided that witching out and having her friends kill her witch instead of being collected by the Law of Cycles was the best way to keep Kyubey from being able to carry out his plan.
After Madoka got her powers and memories back, got through to Homura, and blew up the barrier, Homura was still very much in the mindset that Madoka being the Law of Cycles was Madoka suffering for everyone else instead of being happy, so Homura somehow overloaded her Soul Gem on Love instead of Hope or Grief like they normally use, got a bunch of new super powers, broke Madoka in half, leaving a non-sentient, partially functional Law of Cycles out there and an amnesiac Madoka who was just a normal girl. She then used her new powers to put the entire universe inside a barrier, created a ton of familiars to kill Kyubey's various bodies, and erased all her friends' memories of what had happened so they could go back to being normal girls inside a universe she controlled.
All the while Clara Dolls, Homura's familiars, spend their time jeering at Homura, and basically acting as an externalized version of Homura's own self-loathing.
