Centuries ago, the Queen of the Sun and the Queen of the Moon protected the earth from all forms of ancient evil with help with their Guardians of Harmony. But after battling against the forces of evil for so long, the Queen of the Moon became corrupted and attempted to cover the world in darkness. But after battling the Queen of the Moon, the Guardians of Harmony defeated and sealed the Queen away. Ten-thousand years have passed and the seal is starting to fade.

After graduating high school, the gang from Equestria Girls are ready to take on more challenges then they can possibly handle including new threats making it's way from Equestria, finding out who they really are, falling in love and the toughest challenge yet, College.