Told from the modulating viewpoints of 15-year-old slave Amari, and 17-year-old indentured servant Polly, Copper Sun is a story of resilience in the face of human depravity, and a hope for freedom against all odds.

When the novel opens, Amari is a happy teenager, engaged to the most handsome man in her African village, and beloved by her parents. When white men enter her village for the first time, her people welcome them with open arms, but the men are here for violence. The white men shoot and kill most of Amari's village before setting it aflame. They chain and shackle the healthy youth and cram them into a slave ship set for America. A terrified Amari is sold to Mr. Percival Derby as a birthday present for his eldest son, Clay. At the same time, Mr. Derby purchases the indenture of a seventeen-year-old girl named Polly, who has 14 years left on her service before she earns her freedom. When Polly first meets Amari, she doesn't want anything to do with her. Polly feels superior to Amari because Polly is a white girl who will eventually be free, while Amari is a black slave, no more than a beast of burden in many white people's eyes.

Life on the Derby plantation is horrendous for both girls, and in time, they forge a bond based simply on their will to survive their terrible condition. This bond strengthens after Clay begins raping Amari and Polly sees first-hand just how scare Amari is, which is the same reaction Polly would have to the treatment. She realizes that blacks, even though they are slaves, have the same emotions, and are just as human, as their white slave holders. The only respite for the two young girls comes from the feisty humor of Mr. Derby's slave cook, Teenie, the unbreakable precociousness of Teenie's four-year-old son Tidbit, and the secret kindness of Mr. Derby's eighteen-year-old second wife, who is nearly nine months pregnant. When Mr. Derby remarried after his first wife passed away, his teenage bride came to her new home with all her belongings and her favorite slave, Noah. When Mrs. Derby goes into labor on the plantations, the slave women, including Amari, quickly rush to her aid. Amari is horrified when she sees that Mrs. Derby's baby does not share the white skin of Mr. Derby, but is a beautiful caramel brown, the same color as Noah's skin. Mrs. Derby admits to the girls that she and Noah are deeply in love, and she begs them to help her save her baby. All the slave women band together in an attempt to hide the truth from Mr. Derby, claiming that the baby was stillborn and had to be quickly buried, but Mr. Derby demands to see the body. When no one can produce the dead child, Clay searches the slave quarters and reveals the truth: the baby is not dead, and the baby is black. Mr. Derby calls all the slaves to the courtyard and forces them to watch as he shoots the newborn infant in the head. He then turns the gun on Noah, instantly killing him too. For their part in covering up the truth, Amari and Polly are whipped, held overnight in the storage room, and promised that in the morning, they will be sold to the nearest brothel.

The next morning, the girls manage to escape. They grab Tidbit and run wildly into the woods. The trio run until their legs tire, heading South toward a land known as Fort Mose, a Spanish colony in Florida where slaves can be freed. The trio run for two months, braving every imaginable danger from wild animals to starvation to the appearance of evil Clay Derby who has come to reclaim them. Through all their trials, the three children must trust and depend on each other to survive. Skin color is no longer an issue and the children view themselves as equal. They meet many kindly strangers along the way who help hide them, give them food, and assist in transportation. Finally, the three weary travelers reach the gate to Fort Mose, where they find a sense of security, safety, and above all, freedom from slavery.