When I first read the post, I thought of Monte Cook's Banebrute creatures from his latest pdf "Banewarrens." This disease or virus is changing raised creatures into something else entirely, days after the ressurection event. They are then mysteriously lulled to an unknown location, and for what grand unknown purpose...
The PCs are dragged into the event because, as adventurers, most if not all of them have been raised at one point or another.
The creatures created do not have to be "brutes", but there are slight physical changes and an allofness about them. They may even seem to say they are in charge, but their actions dictate otherwise. Groups of disparate creatures that normally don't work together do so, unconscciously, without even needing to share a language.
In their investigation, they find a group of evil cultist, who kill innocents in order to raise them up, to add to the army of unliving.
From various contacts, the PCs learn that, this virus is affecting people eqi-distant from an epicentre at the same time. There is a centre. an emanating spot of this horror.
What will they find? An evil cult? A group of necromancers using a true ritual, one that all lesser raise deads/ressurections are based on and can thus pervert? An good aligned undead priest frozen in time, unturning a creature of great power? An astral gate, which should be sending souls into heavens, is spewing forth this virus? Or an epic druid, tired of the reckless use of raise dead and the havoc caused to nature casting an epic spell of vengeance. Or something truely unique... a Poisoned Wel of Life. A cursed fey mound? An inverted altar of birth and resurection?
Thanks for the great idea EH! I'm not sure what you will do with this, but I know my players will eventually face this.