First you have to have a complete understanding of the project, the universe it takes place in and the players involved. Also keep in mind what themes, concepts, and messages you want to portray in this project. Understand what you want to accomplish with this project, and to what category of audience you are aiming for. You then should have a broad outline of the story that plots the start, middle and end; also keep in mind the feeling you want the reader to have at the end of the story. After you have the outline you should start filling in the details of the story, fleshing it out over and over until you feel comfortable with it.
Characters are very important, you want your characters to have depth and not be one-sided, shallow characters. You want your characters to be living breathing beings, who bleed, cry and have feelings; it helps to have relatable characters, especially if these characters live in a fantastic universe. Keep in mind the way your characters react to the universe they live in will determine how the audience will react to it.
Research the components of your universe: weapons, vehicles, creatures, clothing, technologies, magic etc. No matter how fantastic your story is, it should have anchors in real life elements.
Do the science behind the art of storytelling, research script and screenplay writing online. Reverse engineer the stories and movies people regard as the greatest stories off all time, find out why people love these stories so much?
Don't be afraid to experiment and play with new and innovative thoughts and concepts, don't just re-create what has already been done.
Look at your project as a thanksgiving feast, and not a microwave dinner. There is enough garbage out there already, don't be a part of that, be the great creator you know you can be. The more you put into your project the more you will get out of it.