Now that you are organized to never lose a frame or element of your animation, you are ready to focus on what you want to do. You want to tell a story.
Whether you are setting up a game, doing scientific visualization, or making an animation to show on YouTube, odds are that there's a story involved. And I'm sure you want it to be a good one. I can't give you all the rules here. According to Gene Deitch, director of Tom Terrific, Tom and Jerry and Krazy Kat cartoons, you start with a premise, or an idea. The premise breaks down into three parts, a character, a conflict, and a resolution. Think about how your favorite animation breaks down into these three parts.
There are plenty of books and online sources, and the following is a list of a few of those.
Note
Sources for creating stories for animation
Story - What's it All About? available at http://www.awn.com/genedeitch/gene-deitch-how-succeed-animation/part...