Man, I loved that game (the DOS original)! I don't remember the baddies being Nazis, but it would fit what I do remember from the rest of the game.

Just looked it up (it was originally called "Wolfenstein 3D II: the Rise of the Triad"):

In order to keep as many of the numerous game assets the team had already created from going to waste, Tom Hall came up with a new storyline which still incorporated the Nazi themes seen in the Wolfenstein series, however they would ultimately depart from plotlines involving Nazis, with the final narrative concerning a cult apparently inspired by the Californian folk legend of the Dark Watchers or 'los vigilantes oscuros'.

Neat!

Edit: aw, man, quote your sources, ffs!