Just a heads up dev; a dark story is fine, maybe good even if you do it right BUT killing off love interests/harem members is an absolute hard line in the sand that you simply do not cross. It's not an idea that anyone is clever/edgy/revolutionary for coming up with. I've seen more than one VN crash and burn and lose basically all its players and all interest after trying something brainless like that, and another VN dev that started a shitstorm in the comments just for thinking about doing it.
I have no idea if you're even planning to do that, but let me be abundantly clear: it's not good storytelling. It's not some daring idea that other writers are too scared to do. It doesn't matter what kind of mental gymnastics one goes through to convince themselves that it's a good idea and that they're the one to pull it off: no. You're wrong. You're simply just wrong. And the justifications for thinking it's a good idea are all wrong too.
You have to understand why the vast majority of people come to this site and it's to experience lewd stories. Hence why all the "no sexual content" games find almost no interest. So, if you include stuff in your games that takes away from the lewdness, all you're doing it shooting yourself in the foot and the experience of playing your VN can only suffer for it. That is unless you're EXPLICITLY trying to cater to weirdo snuff/necrophilia fetishists, but the same thing would be true then because the vast majority of normal players would still be disgusted by that. It doesn't matter how many times you repeat that "this dark story won't be for everyone" or whatever; IF you do that, NO ONE will like it.
I truly hope you succeed with this project, and I hope you steadily improve to the point where you can pull this all off. Just, don't make this one mistake and you have a decent chance at it.