crack theory time!
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zecora is, in fact, the new villain!

her convenient alicorn-only potion means she's got to know a lot about the sisters.
she wants the contents of that box, but since she doesn't have the power of an alicorn or the elements, she's been, and will continue to work from the shadows. through subtle manipulations, she'll guide twilight to just enough information to make her perform the actions she can't, then swoop in and snatch her prize at some critical moment!