The Return of Queen Chrysalis

From Equestripedia, the Archives of Equestria!
Cover art by Andy Price

The Return of Queen Chrysalis is the first storyline in IDW Publishing's Friendship is Magic comic series and lasted from #1 to #4. It was followed up by Nightmare Rarity starting at #5 and was the first story since "A Canterlot Wedding" to feature Queen Chrysalis as a character.

Synopsis

Queen Chrysalis, after being defeated, destroyed a small town and built a new Changeling Kingdom in its ruins. Afterwards, she sent an army of Changelings to invade Ponyville and kidnap the Cutie Mark Crusaders to lure the Mane Six into her trap as the Secretariat Comet, a comet that boosts the magical power of all creatures in Equestria flies over Equestria.

After a long journey, the Mane Six get to her new castle and face off against her, but she quickly imprisons them all but Twilight Sparkle. Empowered by the comet, Twilight handily defeats Chrysalis and the day is saved.