In the end, I find that projects like OP describes often are poorly managed and perhaps even lacking some kind of internal agreement and communication in general.
It's worse than that, because most adult games are made by a single person. Therefore they have no excuse. If something appear suddenly in the story it's necessarily their fault ; either they totally failed to introduce it by small touch, or they just thought about it right now. In both case it's not a good sign for the future of the story.
That one don't know his full story from start to end isn't a problem. But, since most of them aren't professional writers, they should at least know all the key moments, in order to anticipate them and make the story progress from one to the other, instead of jumping from an idea to another. It's doesn't matter if the player can't understand what will happen, as long as, if he go back on the story once he know, he can then find at least some of the clues left by the author.
Something as big as what OP took as example can not appear suddenly. That the discovery is a big shock and lead to a sudden understanding of how big and dangerous the menace is, why not. But there's necessarily some signs, or else it mean that they started their big plan few days ago, and the menace will be eradicated relatively easily.
Obviously, one could answer that the signs where present, but that the MC don't knew about them. Yes, it's a possibility. But the player isn't the MC, the signs should still be shown on the background ; strange behavior on the back of the MC, some strange news on the TV, random NPC talking about it on a coffee shop, and things like that.
The TV news can be just a headline, "Still no hope for a cure regarding the recently discovered virus", the NPC can talk about this guy they know that had a sudden behavior change, we (player) can witness a glitch in reality while the MC is walking down a street. It's not enough to spoil the big surprise yet to come, but at least we would know that there's something approaching. And, like I said above, when going back to the start of the story, all those small events now obviously lead to the terrible revelation and, "yes, now that I know, it all make sense".
And those words are the more important. Unless it's a voluntarily move, the story should make sense. And, whatever how stupid, impossible, or unrealistic, it is, if it's introduced slowly, small touch by small touch, it will make sense. But when it's a voluntarily move, it should regard the whole story ; it's a senseless one, dot.
If it regard only one part of the story, or one event, then it totally kill the story. This especially if the story wasn't this great at start and people where mostly playing for the "adult part". In such case, anything that come between the players and the girls, everything that unnecessarily slowdown the progression, will feel like a pure annoyance.
It's by example what happened for
A Wife and Mother, when the MC started to face blackmail after blackmail, and what I fear will happen to
WVM, with the bad guys not going anymore some background annoyance, but a frontal threat. In both case, the writing isn't good enough, and it happened way to late in the story. This late in the story, the players now have their habits, liking either the story or the dose of "goods" it provide ; sometimes both. Suddenly changing both rarely works as expected.
To keep WVM, passing from "the story of a stud that will build a harem with the help of his girlfriend", to "the story of a guy that will join a secret society to help people, partly with his dick", was already hard to take. But it now being, "the story of a stud that will build a harem, while helping people with his dick and fighting bad guys that are really villain peoples"... What next (I only play it when a full day is finished) ? He'll soon run for presidency, then decide to unify the world, in order to start human expansion in the galaxy ? :/
At the opposite, there's a game like
Fetish Locator. The fact that the application is also used for blackmail, then the fact that someone is investigating this, were near to deus ex machina moves, but they don't change the story. It's still the story of a student exploring sexuality with the help of an application ; just that now he don't do it just for his pleasure. It also haven't changed the pace of the story, because there's no need to extra scenes especially wrote to deal with those addition to it ; unlike for the two examples above.