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The theme of your story is its underlying issue, the thing it's about, the moral at the story's core. Theme is what transforms the film from a collection of interesting scenes to a unified whole. Theme gives the story its spine. It's the glue that binds.
Think of your theme as a thesis that your protagonist will prove either right or wrong. In Casablanca the theme is self-sacrifice for a higher purpose. Humphrey Bogart goes from insisting that he sticks his neck out for no one to sacrificing the woman he loves so that they can all battle tyranny. The theme of Wizard of Oz is, "There's no place like home." Common themes include "Crime doesn't pay," "Power corrupts," and "Reality is illusion."
How do you come up with your screenplay's theme? Sometimes theme is present from the very start, sometimes it emerges as you write. Each writer has a source of inspiration, an aspect of life that fascinates her and that she explores through her writing. Usually, your theme springs from that well. If you've chosen a story you truly believe in, the theme will become apparent.
Once you are able to articulate your theme, use that knowledge as you rewrite. Every scene, character dilemma, and event should either speak to that theme or contradict it. (See tip #36, Subplots.)
In many movies, the theme is stated outright early in the first act. How blatantly or how subtly you do this depends on your sensibilities and on the kind of movie you're writing. Be careful, however, not to use the theme to bash the audience over the head with a message. To loosely quote Samuel Goldwyn, movies don't deliver messages. Western Union does.