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Everybody else within Homura's labyrinth had their memories altered, except for Sayaka and Bebe. Why was this?

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It was because Sayaka and Nagisa (aka Bebe) came with Madoka and were entrusted with Madoka's powers and memories.

When Madoka went into the barrier she knew it was a trap set by The Incubators as such she entrusted her powers and her memories to Sayaka and Nagisa and fool The Incubators.

It's revealed that Madoka, Sayaka, and Nagisa didn't have their memories altered by Homura's barrier. Instead Madoka entrusted her memories and powers to Sayaka and Nagisa in order to fool Kyubey. Sayaka and Nagisa simply played along with the barrier while waiting for the right time to reawaken Madoka. Sayaka admits that while it's caused them quite a bit of trouble, Homura has been trying hard and deserves her reward.

Source: Rebellion/Synopsis - Part E (Second Paragraph)

It is hinted beforehand that Sayaka has extra knowledge as after Homura and Mami fought Mami remembers that their enemies were the Wraiths not the Nightmares however Sayaka remembers the Witches and that Bebe/Nagisa is taking the form of the "Desserts/Sweets Witch"1 (understanding why Homura suspected her to begin with). she shouldn't know what Witches are however because in Madoka's Universe they don't exist.

Also because they played along there was no reason for Homura's labyrinth to try and alter their memories, but i also like to suspect the divine nature of Madoka's powers that they had been given provided some protection since the barrier was one way and only invited people in. Madoka was invited and maybe Sayaka but Homura would have no knowledge of Nagisa and even if she went in as Bebe (thus looking like Charlotte's first form) she was never invited in and i would think that the barrier would try something at first but when Nagisa played along it then just decided to factor her in

1: Depending on what version you see Sayaka will call Charlotte the Sweets Witch or the Desert Witch

Memor-X
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  • Why didn't Homura alter their memories though? Why would they want to play along and feign ignorance of the situation if they could solve it? Kyouko's, and Mami's memories were altered in a way that made them think they lived a completely different life, so why weren't everybody else's memories altered in the same way? –  Oct 04 '15 at 21:55
  • @Christian their job wasn't to stop Homura but to look after Madoka's powers and memories until the time came that she could free Homura from the Incubators thus allowing herself to purify Homura's Soul Gem without the Incubators containing and manipulating her (as to their plan). Homura's barrier only acted in defence as when Homura and Kyoko figured out that they can't leave the city the minions were converging on them but when Homura said they should act like they know nothing the minions began to disperse. – Memor-X Oct 05 '15 at 06:52
  • (Cont.) Sayaka and Nagisa were doing nothing to disrupt the ideal lives there thus no action was needed but wether the barrier knew they were faking or not I don't know but I suspect they had some protection with Madoka's powers they received, as I state in my final paragraph. it's possible that the Wraith Arc manga might explain this at the end but I havn't read much on it just yet – Memor-X Oct 05 '15 at 06:53
  • Why, then, didn't Madoka just get it done in one shot? They were afraid of the incubators controlling Madoka, sure, but it wasn't hard to figure out that Madoka was the "god" that they were looking for. If the incubators were going to find out who she was eventually and it didn't really matter whether they knew who she was at that time or not, she could've just done it at the very beginning and gotten it over with. –  Oct 05 '15 at 21:27
  • @Christian The Incubators don't know *who* was the Law of Cycles and theorized that it was Madoka because she appeared in Homura's barrier and yet did not exist anywhere in history and was not one of Homura's Minions thus concluding that Madoka somehow existed to Homura but not to the rest of the universe. Also Madoka could not purify Homura's Soul Gem outside the Isolation Field so she had to go into it, the Incubators were fairly confident that once they had the *Law of Cycles* she wouldn't be able to escape. – Memor-X Oct 05 '15 at 22:04
  • (Cont.) once inside the Incubators could then observe the Law of Cycles do it's thing, learn to interfere and eventually control it allowing Witches to return and the undoing on Madoka's wish – Memor-X Oct 05 '15 at 22:04
  • Well Sayaka and everybody had to break the incubation field anyways, so why wouldn't Madoka help them out with that at the first chance she could get? I just don't see the point in waiting how long they did to finally take action. –  Oct 05 '15 at 23:23
  • @Christian Madoka's Memories and Powers were given to Sayaka and Nagisa *before* they went into the Isolation Field and Barrier. as for why they waited until Homura became Homulily maybe it was only at that time they could break though Homura's barrier and destroy the Isolation Field from inside the Barrier without the Incubators interfering....or maybe subconsciously Madoka wanted to spend time with Homura before she returned to being the Law of Cycles (as when she returned how much time could they spend together to just relax) – Memor-X Oct 05 '15 at 23:29