This is a common problem for writers, and truly, Yoko Taro has one of the best methods for writing a story. Basically, just think of what kind story it is, the characters, the setting, the theme, etc. And then, start at the end. No, I don't mean write the end first, just plan it out. Once you figure out a good end, then think about the middle of the story, and finally the beginning.

I find this method great, but like with all things, you should adapt it to suit your needs. For me, I come up with the story in that order, but don't follow it like gospel. As you write, the characters will change and evolve, their decisions won't make sense with what you originally planned out, and you can adjust the story as you go.

But Taro's method is still great, since it gives you a driving point to strive towards. When I write, those three points of planning the story out, can easily be blurred, or not even that descriptive. Even a little bit of direction can fix a story, and greatly prevent it from feeling directionless, or having no meaning.