Since I play original WoW, I had this idea so here it is
I guess everyone is a little bit familiar with the lore of Azeroth, so I don't start to explain the whole storie.
Twilight arrives to Azeroth, and she becomes involved in the battle of immortal alicons (mostly because her name
). The Aspects of Life, Time, Dream and Magic seek to defeat their enemy, their corrupted brother Neltharion, the Earth-Warden, now Death Wing, the Destroyer. Death Wing see Twilight's arrival as a sign, that this is his time to release his new powers, kill his former brothers, sisters and cover Azeroth into "an eternal night and darkness".
The ide was given to me by the season opener and Luna's transformation into Nightmare Moon
The red, green and bronze flight are normal ponies, the blue and black flight are night-breeds (mostly that's why the blue flight got nearly destroyed, since they were in closer relation with the black flight).