In brainstorming a work, you will often find that you want your characters to behave in certain ways. And as they grow and develop, you may even find that you need to justify why they do what they do. If you get deep enough into their thought processes, you can almost imagine them arguing with you. When that happens, go ahead and find a way to put that argument down on paper, either as internal dialog or in a conversation. It shows that your character is conflicted about something. It often is a point at which a "theme" begins to grow out of your story.
A theme is simply an intellectual argument--played out in the deeds, thoughts, and discussions of your characters--that throws light upon a topic that has real life implications for your characters.
A famous screenwriting consultant, story doctor, author, and producer named Michael Hauge often gives seminars in Hollywood, and I once heard him make an interesting point. He said that he has never seen a movie or read a book that worked where the question of the protagonist's identity doesn't come up. In short, questions like "Who am I?" "What am I?" and "Why am I this way?" are at the core of every great work.
For example, let's say that you have a young hero who meets a woman and falls in love. She has to wonder if that young man would be proper husband material. Her father and mother might look at the young man in question and give numerous and valid reasons as to why he is not. His own tenderness and thoughtfulness toward the young woman might form the nucleus of an argument against the parents' objections. He will of course have to ask himself this question and decide whether to propose. In the end the young woman--and the audience--must make their own decisions.
This whole question of identity seems to lie at the core of every romance that you will ever come across. Because it is so central, the male is often presented as a "mysterious stranger" at first, someone who is reclusive or often called away upon some earth-shattering business--either to consult with royalty or fight in a war.
But as you plot, it might be well to consider: What roles must my characters try to fill in this story? Do they fit into those roles easily, or do they question themselves? Do others question their ability? What conflicts will arise because of this? What must my character do in order to convince himself, others, and my audience that he or she is fit to assume the roles that they must fulfill?
I'm not going to go as far as Michael Hauge and say that such questions lie at the heart of all great fiction. I can see a couple of ways to get around it. But it is a powerful tool for generating stories.
I have a short story set in the Runelords universe that is up for free today. Get it here.