After Twilight was summoned to take part in her very first Princess Summit in the Crystal Empire, her crown was stolen by two mysterious ponies who took it with them to another world.
In order to get the crown back, she and Star Twinkle decided to go to this other world in order to bring the crown back to Equestria. But soon they found themselves in completely different bodies and a world that they yet had to understand.

This story takes place after Season three of My Little Pony - The Legend of Friendship (After Chapter 65) and is a rewrite of the first Equestria Girls movie.
To put it short: The story of My Little Pony - The Legend of Friendship involves around a stallion added to the mane six and several other OC who were added to the original story of Friendship is Magic.
It is advised to read through Chapter 1 - 65 if you want to read this story in the original order.