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.
Immediately following The Beginning of the End, Fluttershy is ponynapped, and Discord disappears. All of Equestria now hangs in the balance. (A Fluttercord tale)