In the years following the crowning of Twilight Sparkle as Equestria's ruler, a race of extra-dimensional beings, called The Combine, invade Earth and easily overpower her peaceful regime. The Combine take the form of the native life in an effort to ease the distrust against them, but it doesn't seem to work. Twilight flees her palace and enters hiding as she watches her kingdom crumble to ruins, and as the era of the Combine takes root.

Fast Forward about 20 years to the present day, the past Equestria is forgotten, and Twilight has disguised herself as a normal civilian in an attempt to keep The Combine off her back. She must now pick up the pieces, and find the ones she once knew as friends.