Immediately following The Beginning of the End, Fluttershy is ponynapped, and Discord disappears. All of Equestria now hangs in the balance. (A Fluttercord tale)
In the moons since her captivity under King Sombra, Fluttershy is expecting a foal. She worries it will be a shadow pony like its father, and what she learns about dark magic drives a wedge between her and Discord.