So we finally discover the full truth behind the magical girls: It’s a process used by Kyubey aka. The Incubator in order to gather energy from the emotions from teen girls in order to prevent the heat death of the universe. As a result, all magical girls, eventually, become witches, and when that happens, Kyubey can gather their energy. He is so intent on having Madoka become a magical girl because, with her latent power, she would provide an extraordinary amount of energy toward Kyubey’s goal.
As Sayaka and Homura noted, balance in the world has to be maintained, which means that the wish that is granted has to be repaid via an equal amount of negativity in that world, which is accomplished by the despair of the magical girls and the curses they cast once they become witches. The bigger the wish granted to become a magical girl, the more curses they cast as witches.
While Kyubey may have seemed cute and innocent at the start, it’s now clear he’s just using humanity to further his own goals, even going so far as to mislead Sakura into believing Sayaka could be saved, resulting in her death, putting Homura and Madoka in the position where, the only person who can save the city from Walpurgis Night is Madoka if she turns into a Magical Girl. If he can’t trick her into becoming a magical girl, then he’s going to try to coerce her into it by threatening everyone she loves with destruction if she doesn’t.
Speaking of Sakura, she’s come off as a bit better character in these episodes. In a way, she and Sayaka aren’t very different: they both made wishes to help others, only to have those wishes turn against them. Sakura decided to turn her despair into a philosophy of doing things only for herself while Sayaka just gave up and became a witch. In any case, as Sakura mentioned, the only time becoming a Magical Girl makes sense is if you have nowhere else to turn, such as when she was living in abject poverty or when Mami used her wish to save herself from death.
As for Homura, she appears to know everything because she’s able to use time manipulation. Whether that means she’s able to go back in time and “start over” whenever she fails, I’m not sure. All we know is that she’s from another timeline. She may not be able to go back in time within the same timeline, though she is able to pause time. One would think this will eventually come into play again in the final three episodes.
It seems likely that Madoka will eventually become a Magical Girl under some circumstances. For example one wish that was suggested by Kyubey (even though he said he couldn’t make suggestions before) was for her to become an omnipotent god. Perhaps with such a wish she could avoid the heat death of the universe herself, and perhaps change her fate of becoming a witch that way.