I'm leaning that the unnamed entity who overwatches the gods is going to be the final encounter in the third raid. In fact, I'm placing money down that the ending to this entire raid, and I can see it coming from a mile away, is that the gods are setting themselves up to basically die and get recycled into the aetherical sea to become mortals. That's what they're dreaming about essentially.
The MSQ, however, I have no idea how the hell they're going to wrap that arc up in 6.4. There's two ways I see that going down; one, either they flood the thirteenth with light and grant the denizens death basically. Or two, they find a way to purge darkness and reverse the corruption restoring the denizen's original forms paving way for 7.0. I genuinely have no idea what they're setting up.