The way Queen Chrysalis operates is vastly different in the Chaos is Magic storyline, however this is due to the interesting direction the girl playing her has gone. In her storyline, the Changelings are actually the Flutter Ponies cursed many years ago. This came as a result of noticing similarities between the two races. Originally, the Sun Stone was diminished, and the Flutter Ponies created the Crystal Empire to help refract and amplify the sun's power to make up for the absent Sun Stone.

However, as we know, King Sombra took the empire and the Flutter Ponies became victims of his curse, becoming horrific monsters we know as Changelings. Chrysalis is in fact Queen Rosedust, hardened and cruel by her time as a monster. She managed to take back the empire by defeating Shining Armor and kidnapping Princess Cadance while Discord occupied them with his own attacks. After a long struggle, Shining Armor made it into the castle, now turned into a giant hive full of changelings and was forced to confront Princess Cadance, under control of the queen.

At the same time, the newly resurrected King Sombra sought out Queen Chrysalis and fought her, wounding her and leaving her unable to fight back. She escaped by the skin of her teeth, but lost Cadance to Shining Armor. She remains wounded, but recovering slowly. However her fighting spirit is reduced to nothing ever since she lost her control over Princess Cadance. One can only wonder why...?