Strife has been building between Princess Celestia and Princess Luna for years, differences in opinion on ruling have finally caused them to part ways. Realizing that Princess Luna and Princess Celestia aren't perfect, and have both made questionable choices, even if they have all turned out alright, and seeing the argument that caused the final rift between the sisters have led Twilight to also succeed from Equestria.
Now Twilight must rally the ponies of Equestria under her banner, and hope to bring peace and harmony to a land that is beginning to shatter from the strain of a three-way civil war.