At the end of the book Will chooses to stay on the farm.
Will is an orphan of the Civil War. His father and brother died in the war. His mother died after the war. His sisters died from typhoid. Will blames the Yankees for all of these deaths and the damage they brought to the South in general. He is sent to live with his Uncle Jed.
Your uncle wasn’t a traitor. He didn’t help the Yankees, he just didn’t fight them. (Ch. 1)
However, Will disagrees with Uncle Jed because he feels that Uncle Jed is a traitor. He avoided the war, and helped a Yankee Soldier. So he does not want to live with Uncle Jed, who also has a daughter named Megan only two years younger than Will (she is ten and he is twelve). There are also twin boys who left to look for work because Uncle Jed is very poor.
Even though Will resents his uncle’s politics and doesn’t like farm life, he feels bad that his aunt and uncle have another mouth to feed when they are so poor. What little they did have was conscripted by the Confederate army, making him feel even more conflicted. He even befriends the Yankee soldier his uncle takes in. His uncle explains that he disagreed with the war on principle and with slavery in particular.
So when Will is given the choice to go to live with Doc Martin or Uncle Jed, he chooses to stay with his blood.
[Doc Martin] said it was up to me, but he was sure my mother would have understood if I’d rather live in Winchester instead of here in the country.” (Ch. 17)
This choice demonstrates that Will has grown of the course of the novel. He has learned that although war is terrible, it is more complex than he thought. His uncle’s reasons for staying out of the war were just, and his uncle is a good man.
Reeder, Carolyn (2008-06-20). Shades of Gray (p. 151). Aladdin. Kindle Edition.