With their rise to power the elements of harmony were corrupted by a very powerful and ancient force that turned the mane six to turn into dark forms of their former selves with nothing but the intent to kill.
This mixed in with the miasma (What made nightmare moon and nightmare rarity) made them go on a killing spree throughout Equestria which is currently under a blockade under the command of Empress Cadance I of the crystal empire and the other nations, after Luna’s defeat and death; Celestia, being the only surviving monarch of Equestria approaches the Everfree ponies (A species created by me) who had gone into hiding after many years of persecution by Celestia and asks for their help in exchange for her pardon for a crime commited centuries ago.
Meanwhile the elements of the Apocalypse have unleashed an ancient demon that had been imprisoned under ponyville for millennia and is also destined to bring about the end of the world now that he is free he has unleashed an army of darkness on Canterlot, this army is literally made out of the darkness and shadows; they have the ability to possess the dead, so naturally arrive in large frightening swarms.