Chrysalis plans to revive King Sombra so that they may rule all of Equestria together, but to bring him back she needs pieces of an ancient artifact scattered all across the farthest confines of Equestria.

However, to make sure there's no interference from the Elements of Harmony, Sombra gives Chrysalis some of his magic, which she uses to use the Princesses to stone, and capture both Twilight and Cadence, both pregnant with their respective husbands' babies. Chrysalis also kidnaps the Mane Six and and separates them into different parts of Equestria so that they won't rise up against her.

So it's up to Shining Armor, Discord, Screwball and Spike to rescue their wives, the Elements of Harmony, defeat both Chrysalis and Sombra, and change the princesses back to normal. However, Discord is haunted by nightmares and visions of Twilight dying at childbirth, and this stirs his worst fears of losing her, something of which Chrysalis and Sombra decide to take advantage of.

Will they get to the Elements in time?