Every moment in Rebellion has a counterpart elsewhere in the film; these shots are the emotional climax of two scenes in which Homura comes to a realization after a heartfelt encounter with Madoka - the keys to the rebellion, as it were.
In the flower field scene, Homura has a "flash of insight" depicted visually as the searchlights from the blimps illuminating her. This is a common technique Shaft uses on multiple occasions, roughly equivalent to a lightbulb appearing over a character's head in English-language comics, though it can also be used as "spotlight" for emphasis.
Madoka POV: "Would that be worth trading your soul for?" / "Would you like to?" (She says "yes," btw.)
In the flower field scene, Homura is distraught by Madoka saying that leaving her friends and family behind forever would break her heart when the spotlight hits. Whether this is truly what Madoka with all her memories believes is open for debate - Akiyuki Shinbo and Gen Urobuchi have contradictory answers about this - but either way, Madoka confirms what Homura has always secretly feared (and also what she wants to believe) and we get a brief flashback to their conversation in the skybridge at school which is also foreshadowing that scene's parallel at the end of film.
(According to Inu Curry, the blimps - all named "Lisa" - "rewrite the memories of the humans brought into the labyrinth", so their presence in this scene is significant given how much "real memory vs. fake memory" comes up in this scene. Another implication of the spotlight is that Homura is remembering things she's forgotten - her true purpose, as it were. Remember, "stopping Madoka from the consequences of making a wish" was her goal for most of the anime - the details may have changed, but the emotional core is the same. She can't undo Madoka's wish directly, but she will get creative and find another way to cancel it out.)
Immediately after the spotlight, Homura blames herself for Madoka's disappearance - "I should have stopped you back then no matter what I had to do". The seeds for the rebellion have been sown; everything that happens afterwards is a direct result of this moment. However, Homura has the desire to stop Madoka, but not the means at this point - she will acquire those later, thanks to Kyubey's expository monologue.
In addition, Homura leaves the flower field with two other conclusions - that the Madoka before her is the "real Madoka", not a hallucination or a construction of her own mind, and that Homura herself is the witch trapping everyone in the labyrinth. Both of these things are seemingly impossible, and yet she is correct on both counts, as Kyubey confirms. The test with the soul gem at the bus stop is merely the moment the curtain is ripped away and the last illusion falls - Homura walks away from Madoka in the flower field fully expecting to die, but happy because she was somehow able to see Madoka one last time.
In the scenes that follow, Homura goes through the motions of suicide 3 times - when she shoots her fake soul gem after confirming she's a witch, when she calls down the curses upon herself and accelerates her transformation, and when she marches to the guillotine for her execution. The last one is interrupted by Madoka, but I suspect that if Homura "died" there, it wouldn't actually kill her; her memories would be erased and the whole cycle would "repeat" as a infinite loop, which may have been part of Homura's plan, consciously or not. (Insert "if you die in your dreams, do you die in real life?" debate here)
But then we get to the other key scene - the flower field's counterpart - in which Homura, writhing in the purple goo of despair, has another revelation in response to what Madoka says: "I'd commit the worst sins for one more chance, even if it turned me into a monster." That's what pulls her out of the purple goo and back to her "normal" self. And while it's not shown on screen, I believe that's also the moment Homura's soul gem changes color, transforming the blackness of despair into the color of "love". That's the moment she transcends Kyubey's magical girl/witch dichotomy and becomes a secret third thing - a devil. This is the true climax of the movie, even if the full implications aren't revealed immediately.
This is not the color of curses, to the point where I'm not convinced Madoka could "purify" Homura's soul gem even if she'd made contact with it.
Homura now has the motive, the means, and the opportunity to rebel. Thanks to the flower field scene, she believes Madoka is suffering with loneliness as a goddess, and it is Homura's duty to save her. Thanks to Kyubey's experiment, Homura knows it is possible to physically separate the "Law of Cycles" from the human Madoka and for Madoka to live as a normal girl without her memory. Thanks to her final revelation, Homura has the resolve, which has simultaneously and conveniently granted her the power to do what she wants to do. And thanks to her soul gem serving as lure, Madokami is finally within Homura's reach. All the ingredients for the rebellion are in place, so it happens.
People ask all the time "how did Homura have the power to do what she did" and while it may be cliche, the film makes it very clear it is "the power of love". There are other possible metaphors and explanations, but as far as Urobuchi's script is concerned, it boils down to: Homura was able to transform her despair instead of letting it consume her, because it represents her love for Madoka, and love is a powerful cosmic force akin to hope and despair but without being subject to either, especially in the world inside Homura's soul gem, which she completely controls. By turning her soul gem inside out and projecting it onto the universe, Homura takes over everything and remakes the world as she did before - but consciously, rather than unconsciously.
(I know people want more details and mechanics, and I feel you on that, but ultimately, Urobuchi is not really a worldbuilding guy - the world in his stories exists to make the plot happen instead of the other way around. If you want more specifics, you have to go to someone like Doroinu Curry, who has so much worldbuilding that most of it can't even fit in the movie. But the script comes before most of the lore, not the other way around.)
Through a series of bizarre and improbable events, most of which she could not have known about in the flower field scene, Homura takes the opportunity fate has offered her and does exactly what she says she's going to do. She stopped Madoka, no matter what she had to do; she committed the "worst sin" (for her, anyway) for one more chance, even if it meant turning into a monster (witch/devil). She got exactly what she wanted, which per Urobuchi's theory of character development means that she becomes a villain, but at the same time remains a protagonist because her victory is fragile and she must remain vigilant to obtain it. What a neat trick!
It may be confusing to watch in real time, to the point where I have to keep breaking things down line by line and scene by scene in order to make sense of it, but structurally, at least, all of the pieces are there and every line is serving at least one purpose (often more).
