The real answer, of course, is who Glorious Godfrey is really working for. But I doubt the show will last long enough to show that.
I too doubt we'll see it on the show, but Godfrey
always works for Darkseid. This season of Young Justice has focused on the 25 year old "Invasion"
comics mini-series; and what they are doing with Godfrey is a piece of the comics mini-series "Legends"
from the same time frame. I can only guess that a 3rd season of YJ would have that sub-title as it explores Darkseid's long game.