The story starts out mysteriously for the viewer because we have Homura, Madoka, Sayaka, Kyoko, and Mami having adventures stopping nightmares which take physical form. It's fun, and interesting because when looked at generally the entire first act is a look at what the show could have been if it didn't tackle the deep themes. Here we have a team with flashy Sailor Moon-like transformations, stopping monsters and having tea together afterward, with them even singing a My Little Pony-like song to save the day. Not only that, but Kyubey is basically a Pokemon mascot. It's a "perfect" reality, and quite brilliant. Of course, Homura eventually realizes something is up and goes on a journey searching for the answer.
To me, it was obvious that this was an "ideal" reality. (Shows such as Under the Dome and Falling Skies have done this not too long ago.) What's not obvious is what exactly is causing this. The plot twist that it was mainly Homura's doing was great, but not half as great as the fact it was also Kyubey's experiment. We'll address that in a second, but first it's important to mention the cool things which transpired inside the fake world. Perhaps the best scene was the fight between Mami and Homura. It was well choreographed and just plain epic. The soundtrack throughout the film is as expected solid, but the best themes play right before and during this battle.
The sad part about being just 12 episodes is that some characters just don't get enough satisfying screen time. In the case of "Madoka," just about all the characters were engaging. Kyoko for example only got to appear in a few episodes. So, it was great seeing her get a substantial role here. She has some great humorous lines, especially when speaking to Homura about what the former should or not be remembering. The imagery isn't quite as psychedelic as the show's, (it's still insane of course) but still provides some of the most unique graphics in anime. Scenes with the distorted faces on the people was probably the creepiest thing I've seen in awhile.
Kyubey is a fascinating character and great antagonist. He doesn't consider himself evil, yet with no emotions he manipulates as he pleases. The entire sequence with him revealing what he's been doing to her was fantastic. When she shouted, "You want to control Madoka don't you?!" and then the chase scene the viewer can feel the intensity build up as he explains his plan. Seeing Homrua turned into a witch was a sad, but engaging scene as we see her friends unite to help her, much to the amazement of Kyubey This leads to the would-be best scene of the movie.
Homura has been through a lot in the 12 episodes and this movie. The friendship established between her and Madoka is unparalleled. This is evidenced in the dialogue between them on the hilltop. It's a sad state when your best friend no longer exists physically and you're the only one who remembers, like it was all a dream. That's why the scene where Madoka ascends from the heavens to take Homura with her was so effective. It was closure, plus Homura would be with her best friend forever. The dialogue Madoka speaks to her, "Whatever happens to you, good or bad, you're still you and I would never abandon you. So don't give up. Have faith!" is reminiscent of God making a promise to never forsake those whom have pledged faith, then at the end of the day the person is taken up to Heaven. If the scene above was the ending, it would have been fantastic since it basically ties together everything.
Unfortunately, this is not the case.
In a surprise plot twist. Homura stops Madoka from taking her, and somehow, somehow beats Madoka and becomes a god herself, essentially rewriting time again. Homura actually uses the word evil to describe herself. Let's first look at how this doesn't make any kind of sense. For one thing, there's no way Homura could actually stop Madoka. She's a god, (or concept as the series calls it) so there's no way Homura grabbing her can somehow bend the rules, no matter how you look at it. (The explanation given is pretty poor.) What's worst however is that this move isn't consistent with Homura's character throughout the show and majority of the film. She's a concerned friend whom at the end of the show comes to terms with what has transpired. She vows to keep fighting because it's what Madoka would want. In the movie she fights to destroy the fake reality and stop Kyubey from gaining access to Madoka. And then, when it's time to go be with her best friend, (what she's always wanted) she literally goes insane and (for no reason) turns evil literally.
This not only destroys Homura as a character, it destroys the very foundation of Puella Magi. The show ended with the portrayal of hope. The ultimate sacrifice was made. True friendship prevailed. Love, hope, and faith was evident in the finale as Madoka took the burden for all Magical Girls. The show had some dark turns, but at the end the theme of standing up to the demon's schemes and an act of love standing triumph over them prevailed. That's the core of the anime. Rebellion undoes that ending completely. It out of nowhere makes Homura a traitor, insane, and pure evil. It undoes the sacrifice Madoka made. It in effect makes the entire anime moot.
One could perhaps make an argument that the entire final act was an ingenious plot twist. It is correct to say that it's unexpected. The problem is that there's zero build up and no indication in the anime or film that Homura was on the verge of becoming evil. It is the definition of cheap shock value. It would be the same as a 12 issue comic book where the hero faces torment every issue but never gives up having hope. In the final issue he succeeds at saving his family and friends with the sunset behind him. Then a few years later a one-shot is released where it undoes that. It makes the victory irrelevant. The decision to have Homura do what she did is a slap in the face to the incredible anime, her fans, and the franchise. As the ending unveiled itself and the credits started to roll I could feel this inner annoyance because it completely and utterly disregards Homura as a character and what the anime meant.
Rebellion was one of the best anime films I've seen in awhile up until the final 20 minutes. It had everything a sequel should be: it added without hindering the completed story and provided satisfying closure. There's such great symbolism, emotion, and finality to the scene when Madoka comes to take Homura away. Sadly, what happens afterward turns the film upside down. It is by far the worst ending I've personally seen to anything. The plot twist isn't smart, it's terrible. To put it in blunt terms: the ending is total garbage. There's no coherent explanation given. It takes away the essence of hope, and evil wins. It's hard not to want to watch this film because it's a canon sequel, but it ruins what is one of the best anime of all time.