In this case, there is a faction whose power includes the ability to alter realities on a grand scale, up to and including creation, destruction, separation, and merging. They're not perfect at it, but that's the general power scale we're talking about.
I'm trying to figure out how to fit this faction into my game somehow, to have the player characters (who are nowhere near their level of power) interact with them.
The issue I'm having is that in the past, I've seen this sort of interaction (between PCs and nigh-omnipotent NPCs) done really, really badly. I would like to give my players free reign to do what they please, but I'm afraid that if one does the wrong thing, they'll be wiped clean off creation. Conversely, I don't want to reduce the players to spectators in the grand play of this faction's activities in the Multiverse.
So, I ask the members of this community, how would (or have) you run encounters with such NPCs and kept your PCs invested and involved, without throwing them to the lions or making them meaningless?