The story itself is simple. Mary and the other girls are all expected to wear skirts, all the time. My son found this so outrageously shocking the first time we read the story that he actually stared at me with his mouth hanging open! However, one day Mary wears pants, only to be met with outrage. After a talk with her dad, she wears them again the next day, but happily discovers that some of the the other girls are now wearing pants as well.
There is a page in the back discussing Mary Edwards Walker, who the story is based on. I think that this is part of the appeal, how grounded the story is in reality and how clear cut the disparate treatment is. His favorite part was discussing how Dr. Walker was a surgeon in the Civil War and was captured by the Confederates (but still lived to tell the tale).