People work differently, but I'm most comfortable with starting with a conclusion. I'll try to think about a story right now as an example.
I've decided to do a story about pirates. Space pirates. The conflict is going to be based on the fact that piracy hasn't existed in ages. The world governments control over time has constricted to the point where people are unhappy, so they take to the skies and live freely as pirates. Obviously, because they're living in total freedom outside a system of control, they need to leech in order to survive, which means stealing in this case.
After that, all you need to do is decide where you want to begin, and start writing a flowing story with your final goal of where you want the story to end up in mind.