Set fifteen years after the second Equestria Girls film, Solar Shimmer journeys to Equestria to be taught magic by Princess Twilight Sparkle. At first, she is avoided for being destructive with her magic and for her lack of a cutie mark. However, during her time there, she develops a friendship with four ponies who are all misfits in their own way.

Of course, nothing stays happy forever. To break a period of peace throughout Equestria, Nightmare Moon returns, followed by a massive army of cultists lead by a vicious pony named Nighttime Glow. To make matters worse, Nighttime Glow turns herself into the most powerful reincarnation of Nightmare Moon, ever!