I didn't read the whole thread (sorry, I'm tired, and I probably will later).
BUT, here's a twist.
The pcs have to stop some far realm entites from DOING GOOD.
They don't know why, they don't want the actions to stop, per se, and are likely actually in line with the actions of the dastardly, face eating, tentacled things from beyond who are mind controlling or soul stealing people to do good.
But, they're not doing good nicely. They're hurting people to help others. WHY THE HELL WOULD THEY TRY TO SAVE ALL THE ORPHANS? WHY ARE THEY ERRADICATING DISEASE?
It's as though they're taking every dastardly or good measure to save everyone in this one specific town for no particular reason. Everyone will live, whether they want to or not (sorry old man dying of a painful disease, you get a cure light wounds every single darn day, whether you want it or not).
The "unfathomable" part is not actually having a reason yourself. In this case, good DMing is utilizing the arts of "poor DMing". Usually you should have npcs have motivations and reasons. In this case, good dming means they have no knowable motivations and reasons....no knowable motivations or reasons (knowable to us mortals like human DMs) means that they have no motivations or reasons. They just act.
The DM just does interesting stuff to increase horror, which can be to help one pc in a battle while trying to tpk everyone else.
Another, somewhat debatable hint.... Let the player's conspiracy theories drive what they're actually doing. Either decide, or if you can't decide, flip a coin. Heads the players are right, tails the players are only partly right. Or, just assume that whatever the players figure out (this is sorta cheating, but might be ok depending on the genre and buy in of the players) is always partly right, but also always partly wrong. Unknowable reasons, well...they're unknowable. That's sorta the damn deal.
EDIT: to be a bit more clear. Sometimes it's good to break every rule of gaming. Establish, recognize, and respect those rules on a regular basis. Then, with some very specific circumstances, break them. Break em hard and with some regularity. Every expectation is likely to be wrong. Every assumption is way off. But it doesn't always hurt/screw with the players. Sometimes it is to their benefit.
I'm not advocating being a rat bastard dm. I'm advocating being an overly kind and also overly harsh, and very confusing dm who hurts the understanding of players and their character's of the game, the rules, the adventure, the mystery, etc. but doesn't hurt the actual characters that much.
Hell, in a good far realm adventure, the characters might end up broken and insane, and might never ever have taken a point of damage, seen a villain, killed or looted anything, or even really understood what was actually happening....but they should have a solid understanding of what they THOUGHT was happening...and that thing, well, that thing was wrong.