The turtles went on an adventure in another world to saved it from the evil Kraangs, but for that, they needed to learn more about this new world called Equestria, luckily they meet the Mane 6, now the turtles and the Mane 6 needed to unite and save Equestria from the Kraangs and more enemies that are coming
(The story begins before Karai believes she is really the daughter of Splinter and after Mane 6 meets and defeats Starlight Glimmer)