If you just can't find where the plague is coming from, and you've checked all the floors and walls, and taken my other precautions (yes, it can still happen if the fort was previously contaminated like Nutscaves!), then there is still a solution--because in this case you do know where that plague is coming from, by process of elimination. It's on an object that people have been handling.
So there are two things left to do:
- Take everything to the trade depot or the magma sea (in my case I just picked whichever was closer to the items), forfeit all of it, and start over worldly-things-wise. Your material things are much worse than worthless if everyone who touches them dies. Dwarves might die hauling, but more will rise up to replace them until the item gets to its destination. (That, or the fort will die out.) The plague is by far the mightiest opponent I have encountered in Dwarf Fortress, and there is definitely no dishonor in losing to such a powerful foe.
- Look at people's owned clothes that they are not wearing. My dwarves all sleep in one section of the fortress and have their own cabinets, so this is fairly easy (though a bit painstaking) in my fort. If you find plague contaminant on a piece of clothing someone owns (and this can only have happened if your fort wasn't properly quarantined at some point, like Nutscaves), then you have a somewhat serious problem (as in, the type you can't ignore). You can't sell or move owned items, or give the dwarves any instructions whatsoever about them (except this one): So forbid the item and everything adjacent, and wall it up as in Quarantining your fortress, step 6. The owner will not complain as long as it stays forbidden.
I have lit things on fire in the magma shaft countless times with the express purpose of getting rid of them (and more often, without the express purpose of getting rid of them). The water reservoirs are pretty good too, since you can just forbid and forget items that "fall in". (You just have to re-forbid if it gets un-forbidden at any point, or else the owner will start whining about how he really really wants his tattered left sock that's under five stories of water in the well reservoir. I should probably have built a proper drain on that...)
And so concludes how Armok has learned to prevent and fight the plague. Armok's most important feature in this regard is probably persistence, and open-mindedness, because certainly, Armok found not all of the information available about quarantining a fortress online is correct.