In this world, a council of villains, comprised of Nightmare Moon, Discord, Queen Chrysalis, Cozy Glow, Tirek, King Sombra, and a mysterious boss, have been ruling the lands for many years, dividing it into pieces that each of them control.

During this time, Twilight had been living in Ponyville under the order of her mentor to eliminate Queen Chrysalis, who had been getting more powerful over the years. This led to the spiral of events that force Twilight to confront life changing opportunities, like meeting a group of rebels, that make her question her allegiance.

With unexpected help from the less-evil villains, Twilight finds herself attempting to make a change for the world.