Okay, you're still not being very specific. We can't help you if you don't know what you want help with.
That said, I can sort of guess as to what you might be struggling with. I'm assuming that when you get the idea for a story game, you just start writing it with little planning (could be an incorrect assumption, but I don't have much information to work with). Don't do this. Planning and pre-writing is essential to creating a thoroughly coherent game (for most people; it seems, in my other thread "Your Writing Process?," that some just sort of dive in and it works out well enough).
What I do is make sure I know, roughly, what the beginning, middle, and end of the story should look like. Of course, a story game will have many ends. Thankfully, most story games have two or three real/good/perfect ends, so try to structure your story the same way. NOTE, this is just something to help you keep on track with your ideas. This method probably would work with a massive story encompassing many, many smaller stories in the vein of Endmaster's Necromancer (I just can't help but bring that story up, can I?), but I feel those types of stories are the exception (if a very impressive exception).
Take a look at the thread I started to give you a couple different perspectives on the writing process. Almost everyone did something different, and it was very educational. Hope this helped!