One afternoon, when Twilight and Fluttershy are exploring antique stores, Fluttershy purchases a gem that claims to grant any wish she desires. Some may think she'd wish to have more animal friends, or to have better speaking skills. Instead, she wishes that she could fly like Rainbow Dash.
The next morning, Fluttershy wakes up. Except for one thing. She has no idea where she is, or why every pony expects her to go along with a lifestyle she never knew she had.
As a great unicorn once said, magic does what it likes. Sometimes, it changes all aspects of reality, and tweaks the future.