Disclaimer: nothing I own even remotely resembles this show in any of its incarnation so please no lawsuits, I still need to buy dinner!
This story will be mostly Twilight centric until the second half where the others will have much larger roles. So sorry to those who dislike the purple magic pony, you probably won't like this story. With that, the rest of you enjoy!
It could have, should have been so different. Princess Celestia had seen the signs, how could she not. She had never once in all those 1000 years forgotten about her dear little sister Luna, nor had she forgotten how she had failed to wield the Elements of Harmony to their full potential and so had failed to save Luna from being Nightmare Moon. Instead she had been forced to imprison her in the moon, hoping to either find some other way to save Luna from herself or to find somepony who could truly use the Elements to their full capacity. As the 1000th year deadline drew closer, Celestia began to despair. All of her years of research into magic had only reinforced the knowledge that only the true power summoned by the Elements of Harmony could save dear sister Luna, and while Celestia had found so many ponies that could easily embody the Elements of Loyalty, Honesty, Generosity, Laughter, and Kindness, no pony had ever been found who had the most important part, the Spark of Magic, which was needed to activate the true power of the Elements. She had even started a school of magic to gather the best magic user together in hopes of finding it, but no pony could be found in all those years.
Then two miracles had happened at once that would shake the nation. The first was an explosion of light and color that was seen all across Equestria, the first true Sonic Rainboom to happen since its mythical origins. The second was much more local, and almost no pony even knew it had happened. In fact, had Princess Celestia not been drawn away from her personal studies by the explosion, she might have missed it as well.
Just following the first explosion of rainbow light that brought her outside was another that went off right above her head, along with the sudden appearance of a dragon's head bursting through the roof of one of the classrooms. Wondering what the hoof was going on, Celestia raced up to the classroom and burst open the door, and saw the most extraordinary event of her life since she first raised the sun. She saw a young filly bursting with more magic power than she had ever seen, one of the baby dragons used in the application tests fully grown in an instant, the young one's parents turned into potted plants, even the experienced teachers were powerless before the little filly's magic. But really non of that even registered to the shocked Princess of the Sun, for Celestia saw something far more spectacular than any of that.
She saw the Spark.
And in that instant Celestia had an amazing vision, of this young filly grown and powerful, having tons of silly and fun adventures with a group of others who, along with the baby dragon who just hatched that hour, would supports her though thick and thin and she would return the favor may times over. And most importantly she saw that small group activating the Elements of Harmony with the filly's eyes glowing with power... and she knew.
Celestia knew what she had to do. She had to take this youngster under her wing and teach her all that she knew of magic to prepare her for all the tasks her would face in the near future so that she could succeed where Celestia herself had failed.
Tragically for Princess Celestia and indeed all of Equestria, not all prediction come to pass as we would hope.
AN-CONFOUND THESE PONIES! I can't stop watching them! It's madding and yet I love it! And I can't even talk about it to anypony. AAARRRGGHH!