VIPER has always been an weird and interesting case of a super organization that goes from being the comic relief to 'Why haven't they taken over the world'. I'm also going from the 5E version of things here, but as far as I can tell it hasn't changed that much.
VIPER exists in it's Entirety to make sure that the beings who Started VIPER survive the coming apocalypse. Whether that's cause DEMON causes almost all magic to shift out of the CU, or An alien invasion or extra dimensional invasion or what have you, VIPER is there to make sure that Nama (ancient serpent/ god/ being) survives. The origins of the Council are caught up in years/ decades/ centuries of Nama et al encouraging certain families and peoples and bloodlines to seek them out, accumulating in the search for the Serpents Lantern, which they eventually found. The Original Council of Thirty touched the Serpent Lantern, got a nifty tattoo and a vision of the future from Nama. Nama, and VIPER in general, must survive and Nama doesn't care how they do it.
People being people, of course, this means that there is a conspiracy of idiots and geniuses trying to gain as much of everything as they can, and taking over the world so that they can ensure the survival of the Council and Nama, is just one of the things they keep trying. Who knows, maybe at the heart of it all Nama has set this all up so that when the worst happens VIPER and everyone that opposes them will be the best and strongest there is, thus ensuring the survival of the Earth/ Human (Or Whatever) Race/ Nama and others like him.
They seem to be able to do this because theirs is a global conspiracy that has existed, in it's more organized state, since the early 1950s, the Council touches many things in the world and who is to say how much of any government/ economy/ etc is directly or indirectly influenced by VIPER and the Council and they have the ultimate backing of at least 1 very old supra normal being who doesn't care how ridiculous or dangerous or successful they actually are, as long as they can prevent the coming apocalypse.
I like VIPER as it is, because it can go from goofy to deadly serious in about a half second, depending on the needs and tone of the campaign and the interaction of the PCs with the group.
YMMV of course and your version of the CU sounds interesting in general. Love to play in it to be honest.