Often motivation can be found in a character's past. Yes, that's right, the dreaded back story. This is one place where back story can be the writer's friend. If you place it in the right place and handle it deftly, the back story told in a full flashback scene, can give the reader insight into your characters' motivations.
In analyzing character motivation, you can't forget the character's objective. This is the overall arching goal of your characters. What is it that they need or want? Motivation is an extension of this. Most likely the goal is something that motivates them to behave or not in the case of the bad guy.
One way of looking at motivation is to discover what the character needs on Maslow's Hierarchy of Needs. If you haven't studied psychology, Maslow theorized human beings have basic needs and they have a certain level of importance. Individuals who are on the basest level of need - physiological - can't move up the hierarchy unless those basic needs are met. For example, if you don't know where you're next meal is coming from, you're not going to be too worried about studying Napoleon's battle strategy for Waterloo.
As a writer you can use this hierarchy to determine what your character's overarching need is and this determines her motivation.
Maslow's Hierarchy of Needs (in list form)
- Physiological: air, food, water, sleep
- Safety: shelter, physical and financial security
- Social (Love/Belonging): family, friendship, acceptance in a group
- Esteem: confidence, respect, acknowledgement
- Self-Actualization: morality, wisdom, personal potential
- Cognitive: acquire and understand knowledge
- Aesthetic: appreciate and create beauty and structure
Make a list of all the characters in your story. In a correlating column write down what they want to accomplish in the story. To delve deeper, make a third column listing what their deeper psychological need is - Maslow's hierarchy.
Evaluate your list, do any characters have goals in opposition? Great place for conflict, right? How do the characters relate to one another with their goals in mind.
The more you gain clarity in relation to your characters' human needs, the easier it will be to flesh them out into fully developed characters your reader can identify with and care about.
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Remember writing is a process. Keep writing, keep learning, and celebrate wherever you are on your journey.