I wonder whether you wait with development until some ideas come up in your head or you're sitting silently in your room, staring at your monitor and work hard to come up with something.
It totally depend of the writer and his personality. Someone who tend to be rational will sit and start working on his story, making it appear while writing. At the opposite someone who's more artistic need to let the ideas come by themselves, and slowly grow in his mind, before he start seriously writing. And generally when you're one, the methods of the other tend to never works for you.
Also, how are you planning your games? Do you prepare your story's and character's outlines in advance or do you do it as you go?
Planning the game is the only effective way to go, at least if you want a coherent and consistent story. It don't necessarily need to be a whole plan that precisely describe the story, but you need to know the key point, because you'll have to anticipate them, to somehow show them coming.
Nothing come from nowhere. There's always clues regarding what will happen. In real life we generally don't see them, and have no way to goes back in time to look closer. But in a game it's possible, and therefore you need to include those clues.
Lets say that MC have no luck with girls. He start flirting with a girl, and she seem to like him. Then, after some time, she ghost him out of nowhere. And this happen every single time, with every single girl in his life since he's in college. He remember, Anna is the last girl who haven't ghosted him... Ah, Anna, everyone had a crush on her. And she was so nice, always polite and gentle with everyone, to the point that even a looser like Max thought he had a chance.
What the MC don't know, is that Max is the reason why girls act this way with him. He really thought he had a chance, and even years later is convinced that MC stealth his girl, surely using force and blackmail for this, because he's such a jerk, never a girl as innocent as Anna would have feeling for someone like him. Therefore Max now always have an eye on MC, and every time there's a new girl in his life, he start his scheme. He stalk the girl until he discover who's her best friend. Then he befriend the said best friend and start to talk about this guy he know, who's a rapist in disguise ; who's so depraved that more than once a girl he had sex with was found in a near to death condition. At one point the best friend understand that it's MC, and warn her friend, who then ghost the MC.
In terms of story, the player will soon have the impression that there's a guy who's often in the background, but that he seem to appear way less often each time the MC start to flirt with a new girl. This while, each time a new girl have ghosted the MC, this guy seem to be really happy.
At one point, the MC will also reflect about his love life, and he will surely remember that Anna was the last girl to not ghost him. If he isn't a too dumb MC, he should start to notice himself the guy in the background. Then he'll found himself thinking about Anna without real reason, until he understand that it's because of this guy. he look so much like Max, what make his mind drift to Anna... Wait, he don't just, "look like Max", he is Max ! Why is he here so often ? Oh, I remember, he did the same in college... This until Frank and I had to menace him, because he was spreading lies about me. Hmm, can it be that he continue doing this ? Could he be the reason why girls suddenly ghost me out of nowhere ?
But obviously, in order to do this, you need to know your story. If you just decide that girls ghost the MC without apparent reason, then only at the end decide that it's because of Max, and that Max did it because of Anna, there will be no clues in your game. The story will perhaps feel interesting, but once it will reach its end, and you'll make the culprit and his reason appear out of nowhere, all the good thoughts regarding your game will disappear.
When the MC will start to notice Max in the background, it will be the first time the player see him, and this will be weird ; the MC notice a guy that seem to follow him, but never ever in the X previous update we saw this guy ? What a lame writing.
And the same apply for less important points. As I said, nothing come from nowhere, and in order to anticipate what will happen, to make the story, and the characters behavior, tend in this direction, you need to know yourself that it will happen, and when it will happen.