Tbh, This becoming a series of its own isn't a bad idea. I'll love to see what more you have for this version of the story.

Will this story also has (basically) Sean's eventual transformation to pony like how the main series has, or are you planning on deviating away from this if you plan on turning it a series of its own?

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I think that making this a series would be easier for me and help keep my motivation.

To answer your question. Yes and no, it will be a lot different than what I have planned for the other story. This story has a much different path planned out than the original if that makes sense?