I used to struggle with this, never truly sure where to start. Once I began writing plays I figured out some things that have become very helpful for straight up story writing.
Characters are the main focus for me, because once you have that nailed down the pieces click into place. I always start with a general synopsis and write that down. Then I make up some people to populate the world I just created. I make a separate document with a list of characters and I give them some flesh. I figure out how old they are, what they look like, where they come from, what they love and what they hate. I spend a lot of time developing the characters. Sometimes I write a lot more about a character than I will ever use, but really nailing it down helps drive the story later.
Then I make an outline, placing the characters into the synopsis and deciding what happens and in what order. During this process other character insights will pop up, and I plug my notes into the character outline to make sure I have all of it.
This sounds like a lot of work, but for me there is no story without well developed characters. Character is what drives the plot, and once the characters are solid they will pretty much tell you what happens next. It has helped me a great deal to do that work first, then the writing of the actual story is faster and cleaner and I am less prone to staring off into space because I am not sure what to do next.