The movie starts in an interesting spot where we have all 5 girls together, which is odd considering how the main series ended with Madoka becoming a God. The first thing that was off is Kyouko as she ends up being in the same class as Madoka, Homura and Sayaka. After all, she lives in Kazamino and here we learn she lives with Sayaka, which is extremely odd. The first deduction being the girls can't leave Mitakihara.
One of the things most notable in the main anime series is how mysterious Mami was. We see Charlotte hanging around Mami and so much so that it feels so odd. As Mami calling Charlotte or Belle her longtime friend is so odd. As we recall, Charlotte was the figure in the witch domain that killed Mami in episode 3 of the main series. However, this was an excellent red herring because nobody would expect either of those two are innocent by all accounts. Perhaps the friendship between Mami & Belle is actually genuine. Well, there is still some uncertainty, but at the very least both Belle & Mami are innocent. By all accounts, Mami was willing to fight Homura to protect Belle.
Knowing that Sayaka is supposed to be dead, it makes sense that her and Belle would know. Homura killed the witch aka Belle after it killed Mami. We know Madoka allowed Sayaka to pass away happily. Sayaka offered lots of foreshadowing to Homura because she knows if some witch is responsible they need to be taken down. Kind of the idea is status quo such a bad thing? After all, in the present Madoka, Sayaka & Belle are no longer present. Kind of the idea is the wish that made this resulted in this, is this the end of the world? Of course, it is not natural. Kind of hinting the happiness that Homura truly wishes, is that so wrong?
Though it really was Homura's heart 2 heart conversation with Madoka where we can really see where Homura senses she is at fault. On one hand, she knows witches are up to no good. Madoka is a girl who is beyond kind. In an ideal world, she would never want to make that wish. However, given the events how they happened, Madoka wanted to save Homura from despair, but also every Magical Girl from despair. It seems a lot of this knowledge is lost in the current Madoka. Her conversation tempted Homura and got her to question if Madoka was actually happy with her wish. Although in reality it was a stepping stone to Homura not being able to accept Madoka's sacrifice. As her treasured friend, Homura could never bear to lose Madoka. The fact she could question if Madoka was happy with her wish. Finally, Homura finds out the answer and it is an ugly one for her.
Of course, this movie wouldn't be complete if we didn't have Kyuubey stirring shyt. With Madoka creating "The Law of the Cycle", he wanted to see what would happen to Homura if she was cut off. As we can see by now, Homura truly couldn't carry over the sacrifice Madoka. As we know that while Homura said she wanted to save Madoka from being a witch and losing everything that she wanted. In her hearts she didn't want to lose Madoka. In a very cruel fashion, Madoka hoped to save Homura from despair of becoming a witch because what if she gave up and couldn't save Madoka? She would be a witch. Now with Madoka's wish, she is saved from being a Witch, but now she is gone. Kind of shows that Homura so focused on saving Madoka that in reality she didn't just want to save Madoka from becoming a witch, but she didn't want to lose Madoka period. At this point, Homura would be a Witch & Madoka is a God. This isolation field keeps Homura's soul gem intact, which is why she isn't a witch. Also, despite Madoka being able to enter the isolation field, the outside forces of her being a God don't come into play. This leads to what Homura really wanted because Homura as a witch & Madoka as a God would clash. Very much leads to what Sayaka said that things status quo might be preferred, especially for Homura. These two friends being enemies is just tragic.
Of course, once again we see Kyuubey is so unaware of how human emotions work. As he once again views that Magical Girls should be witches. While he does have a point that Homura wanted to be with Madoka again, this is not what she wanted. The amount of despair that Homura feels is unbearable because she realizes that she is responsible. Though worst she sees that once again Kyuubey is after Madoka. Now a decision has to be made because who knows what Kyuubey will do if Madoka is under the influence of his associates. Homura gives into despair because at this point it is the only way to save Madoka. Essentially, what we had was Homura willing to stop Madoka from being a witch. However, Madoka didn't want Homura to give up and fell into despair. Though losing Madoka is still led to it. Kyuubey's influence was obviously at play here.
Though the real twist is what Homura does at the end. As Madoka should have been able to purify Homura as a witch. As Madoka was connected through all the times that Homura tried to save her, she held the power to be a God. Though in reverse wouldn't Homura hold a similar power? It's her love for Madoka. Homura basically turns into a demon of sorts. At this point, it seems that Madoka is broken off from being a God. Though is she now just a normal girl or a magical girl? Though it seems more likely like before she forgot her purpose. As Homura asks, what is more important order or desires? Though it feels inevitable that Homura & Madoka will clash. Though the tears on Homura face, you can see that she knows it is inevitable that the two will clash. Homura got her wish, but in a twisted way of knowing it won't last. Though seeing Sayaka with Kyouko. Mami with Belle. Homura has given in to wanting the status quo. Now we wait on Madoka for what she will do.