What I understood is that the girls were in a world where they were fighting nightmares instead of witches, and Homu was finding strange that there were 3 characters that were not supposed to exist, belieiving that it was BB creating this situation and, after getting in fight with Sayaka and Mami, Kyuubey answered her that Homura was trapped inside Kyuubey's experiment, which was a space isolating Homu's soulgem from Madoka-goddess area of witch spotting, which allowed it to stay pitch black and increasing in evilness, without being able to become a witch. Then Homura surpassed that experiment barrier and became Witch which entered the false world that was inside Homu's soulgem, creating a witch barrier in that world/ Then the remaining magical girl fought the Homu witch and beat it, so Madoka spotted Homu and was about to stop her from being witch, but Homu took the opportunity to extract the goddess side of Madoka from the human madoka, becoming a devil, which could allow her to create a new world, where she could be in the same world as Madoka while restricting when needed the re-goddessing of Madoka. However this new world now looks way darker than the Madoka ruled one, and the only one that seems to be happy with the situation seems to be Homura (the opposide of what was happening in the Madoka -ruled) . At very end Homu seems to be suiciding (or sky-diving lol) when she got bored of this world. What seems to never ever die is Kyubey, because he's the only thing alive when the world is re-created and got a replacement just before homu jumps,
This indeed gives a different light to the episodes/first 2 movies, but I am sure its not finished yet, since 1. all character seem to still remember what happened 2 We dont know if Homu survives after the jump. 3. They would never let something that brings so much money to finish. I think what this movie wants to teach is that a big love can turn to big hate and vise versa. btw BB says "Camembert" (kamamberu)
http://en.wikipedia.org/wiki/Camamber a type of french cheese, not "cheese"