Outside of the plot, the 'theme' is often used to describe a topical issue that runs through the story, for example, fatherhood, unrequited love, racism. But it can also be more subtle, - that which colors the plot, sets its tone, gives it context, for example, water, the sky, sex, and can often be found in the story's imagery and metaphors.
or
The central idea or concept in the story (Sometimes could be the conflict of the story too)