Distinguish between plot and theme. Plot refers to events that take place in the work, whereas theme refers to what the author attempts to convey by writing about them. For example, the plot of "Star Wars" could be expressed as follows: "A boy whose home and family were destroyed by the ruthless Galactic Empire teams up with a band of rebels to disable said empire's ultimate weapon." The themes in "Star Wars," on the other hand, could be anything you want them to be. Here's a relatively indisputable one: "The passionate will triumph over the dispassionate."
Read your story through from beginning to end. Repeat as necessary until you fully understand the plot. Then write the plot just as above: a single sentence summarizing the work. Based on that sentence, think about what the themes could be. Jot down as many as you can think of, even if they contradict one another. Feel free to write them in the form of morals. If it is not immediately apparent what the author wants you to believe, you may write them as two ideas in conflict with each other. Using the "Star Wars" example, you could write "passionate versus dispassionate" in place of "the passionate will triumph over the dispassionate."
Scan the story again. This time, tag (underline, highlight or jot down on a separate piece of paper) nouns that turn up more frequently than others. Examples from "Star Wars" might be "dark" and "galaxy."
Elaborate on inherent connotations. Let's look at the word "dark." Since before humans picked up pens, they've been afraid of what lies beyond their immediate vision. To a caveman, venturing out alone into the dark meant becoming susceptible to predators; to an author--even a contemporary one--you can be fairly sure that "dark" means something sinister, evil or isolated. If you're lucky enough to have tagged any of these freebies, look at them closely in relation to your theme. The theme in the example was, "The passionate will triumph over the dispassionate." You should immediately see the link between "evil" and "dispassionate," but don't stop there. What about "dark" as another word for "isolation?" Are the dispassionate isolated? Is Darth Vader--the "Dark Lord" himself--isolated? You could make a good case for it, based on the events of the movie. Try to do the same with your story. Don't assume that any tagged word is relevant to your theme in just one way.
Extend keywords in the theme to discussion points. On the other hand, the words you've flagged may not have such obvious connotations. Look at the word "galaxy." Nothing comes to mind, right? So let the theme you wrote down earlier help you. In "Star Wars," the rebels obviously represent the passionate and the Empire the dispassionate, but how is the galaxy related to these parties? You haven't yet addressed what there is to be passionate about. The Empire wants control of the galaxy, and the rebels want freedom to use the galaxy as they wish. Does that remind you of any resources right here on your home planet? Land? Wealth? In order to fully understand the symbol, replace the word "galaxy" with the word "resources." Try the same exercise with the words you've tagged in your story. Based on the theme you've written, what broader meaning could these words have? What could they represent that is essential not only to the plot, but to all human life? Keep in mind that Step 4 still applies: There is not one right answer.
Read the story one more time, mentally replacing your tagged symbols with the word(s) or concept(s) you believe they represent. Are there any that fall apart when you pay close attention to their context? Don't be discouraged. Simply repeat the exercise using another of your ideas.