well this is going to be great when they learn who twilight really is,
part of me hope that twilight is now preggers

Now, I haven't read this story yet, but shouldn't there be an alternate universe tag?

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AU is not, however, appropriate for cases where MLP:FiM has no significant impact on the story. When all characters are stripped of their defining features and replaced with fundamentally different traits and characterization, any and all relevance to MLP:FiM is discarded.