How would Twilight Sparkle and her friends from school defeat Sunset Shimmer in this universe?

All I can think of is Twi wondering why Lyra is so fascinated by Ponies.

Second thought is would there be any actual change between the worlds. For example, Sci-Twi still at Crystal Academy or I she going to Canterlot High cause she has friends there. If there is no change, then it could cause problems since some of her friends are enrolled at Crystal. With that separation and school rivalry could bring drama to the story. As well, will any of her friends try to follow her through the portal after set period of time, be it out of fear or concern.

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That is a good idea. I would like to focus on Crystal Prep and Canterlot High together and see how Sunset would enact her evil plan to dominate both schools.