Scootaloo wasn't always known as Scootaloo, and there was a lot more to her than anypony would've guessed. She isn't 'real' to say. She was grown beside her sister in a tube and are practically genetically perfect. Both were grown to lead the approaching rebellion against Equestria, but she seems much weaker than her sister, and the two are almost complete opposites.
Scootaloo leaves the rebellion with the help of a friend and has to learn what it's like to be an average pony in Equestria. But how can she possibly live a normal life when she knows that one day she'll have to step up against the rebellion as she is the only pony is Equestria strong enough to stop them and her sister.
Note: There will be a really unexpected romance at some point in the story and I have a feeling not a lot of people will like the pairing at all. Meh, I'm still gonna do it anyway. Also, I started writing this story a month ago so some of this writing is my older work and it might be better or worse than the newer stuff (who knows)