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Spoiler

So much stuff in this episode. So Magical Girls are basically liches, how nice. Their souls are the gems, and the gems get tainted the more they use magic. They need to fight witches to purify it. The Witches = Magic Girls that become tainted theory seems to be getting more likely. Homura is once again giving strong hints that she's from the future, and her power seems to be slightly confirmed. It's probably slow down. If it was time stop she'd probably just go on top of the truck. If it was teleportation she'd just warp on top. But she was doing "jumps" to reach the truck, so she can probably just slow down time enough so she can eventually catch the truck, but the truck is still going moving ahead as she tries to catch it.

Homura's also doing a lovely job at tainting her own soul. She's using magic left and right and not even refilling her gem. I bet this will be an issue that's addressed later. She turned Mami's offer down before, and I would imagine it's been a while since she's filled her gem. She picked up something after defeating Charlotte, but I dunno if it was Mami's gem or just the grief seed. I'll look back at the episode now. In any case, Mami's spirit is probably still alive, and Homura probably has it for safe keeping. She knows about the whole gems being souls thing, so I don't think she'd just leave Mami's soul behind to be lost for eternity.

Okay, so let's try to get everything straight here. Kyubey = Mephistopheles, pretty much. He's working with human weakness, greed, in an attempt to take little girl's souls. Once their souls are taken from their body, it'll slowly get tainted by sin. This is shown by Sayaka going over the edge as far as to kill someone else in the name of what she believes to be justice. As their souls become more tainted, they eventually turn into grief seeds, and by that point they become a witch. Then Kyubey continues the cycle. Kyubey wants Madoka badly because her soul is pure, as shown by how much of a freaking goodie-two-shoes Madoka is. I'd imagine corrupting a more pure soul yields better results for Kyubey (and Satan, whom he probably serves under). Madoka's gem would be bigger than others, so it'd probably be able to store more sin. When Magical Girls refill their magic with grief seeds, they're transferring their sins to the seeds. Kyubey then takes the seeds for himself, collecting all the sins from the witch as well as newly acquired sin from the Magical Girl.

Any of you on these forums read Faust? I'd like to get more into detail, but I don't want to spoil a classic for those that have yet to read it. Caus Madoka is pretty much Magical Girl Faust.

Spoiler

Because anything would spoil it for anyone