Shades of Gray is a young adolescent book set immediately after America’s Civil War. The main character, twelve-year-old William Page, finds himself an orphan after the war and is sent to live with his aunt and uncle on their farm in Virginia. William’s father and brother were killed by Yankees; his sisters died of typhoid that spread from the Yankee encampments; his mother died of grief. Because of all of this, William holds great bitterness and sorrow in his heart; he blames the Yankees for the death of his family members.

Beyond his personal tragedy, Will harbors resentment for the Yankee troops that tore through the south, burning homes and farms and spreading diseases like the ones that killed his sisters. These strong feelings make it difficult for him to live with his Uncle Jed, who refused to fight in the war. In fact, Uncle Jed avoided the conscription agents who came to his farm and try to recruit and pressure men and boys into fighting for the Confederate army. Will regards his Uncle Jed as a traitor; anyone who didn't try to defend their homes and families against the Northern troops was a coward.

Doc Martin, an old family friend who looked over William's sisters and mother as they died, agrees to take William to Jed’s farm. When they arrive at the farm, Will is introduced to his younger cousin, ten-year-old Megan, and his Aunt Ella, who was his mother’s sister. They are both very nice to Will, and Will is put at ease a bit about having to live on a strange farm with people he did not really know.  However, when Uncle Jed greets him, Will’s anger and resentment return, and it is all that he can do to shake hands with him. Will vows in his mind, however, to never call him Uncle Jed: he does not want to be associated as a family member with a traitor. Doc Martin leaves him with his new family, and Will tries to settle in. His new home is much smaller and much poorer than where he came from. Used to a lifestyle of relative ease living in a town with slaves to do the work, Will experiences a rough adjustment as he learns to work hard on his uncle's farm.  Determined to keep up and be tough, Will does his best to contribute.  He feels bad that his aunt and uncle have to feed and clothe him when they are already so poor. He has older cousins, twin brothers, but they left to find work in Ohio and help by sending money back to the farm. When Will asks why they do not have any food, crops, or livestock, they answer that it was all taken by the rebel army—the Confederates.  At first, Will refuses to believe that his beloved army would do such a thing, but later he reluctantly admits that it is possible. However, he justifies their actions by comparing it to similar things that the Yankee troops did to the south.

Will often goes fishing with Meg. They run into several local boys from the nearby town, who start to bully and cause problems for them. Most of the time, Will handles them with amazing cleverness, calmness, and wit; however, it eventually leads to a fight.  In the end, thanks to some sage advice from his Uncle Jed, Will is able to forge a friendship with Hank, the leader of the boys who bullied him.

Will's relationship with his Uncle Jed is strained for much of the novel.  However, as the story progresses, Will develops...