Do you think Bierce tries to enlist your sympathies toward either the Union or the Confederate side? Or does the story seem to be focused on a more general theme about the natures of war? Cite evidence from the story.

I see no evidence of sympathy toward one side or the other. This story, written during a time of naturalistic and realistic writing, simply focuses on the way in which things happen. They are cruel (that is the nature of war), and they cannot be changed. Farquhar dies; that is what happens in war. Had the young man who stopped at their house not been a spy, that would not have happened. Had they happened upon the young man's identity, he might have been hanged. That too would have been the problem of war. This is not about who is on which side; it is simply about what happens when people are at war.