The following version of the book was used to create this study guide: Barnhill, Kelly. The Witch's Boy. Algonquin Books of Chapel Hill, Chapel Hill, NC, 27515, 2014. Kindle AZW file.

Ned and his twin brother Tam are sons of the woodcutter and a woman known as Sister Witch. Though no one in their village can tell the boys apart, it is obvious that one is better than the other. The boys build a raft they hope will take them to the sea, but the raft does not float. They are drowning when the woodcutter jumps in to save them. The selfish people of the village shout unhelpful advice, including that he should be careful to save the right boy. When the woodcutter is only able to pull Ned from the river, the villager say he saved the wrong boy. That night, Sister Witch knows that her son Tam is dead while Ned is barely clinging to life. She uses the magic her family has protected for years to stitch Tam's soul to Ned's body, giving Ned the strength to recover. Over the coming years, Ned has a debilitating stutter and cannot read or write because of the presence of the extra soul. The villagers constantly say the woodcutter saved the wrong boy, and Ned comes to believe it.

Meanwhile, a girl named Aine lives in the distant kingdom of Duunin. When her mother dies, her father falls into deep grief. When Aine tells him they have no food and no way to continue surviving, her father rouses himself and leads the way into the Deadly Forest that lies between Duunin and Ned's village. There, he finds the cottage where he lived before marrying, and he retrieves a magic pendant that allows him to return to his life as a craft thief. He is soon surrounded by bandits and becomes known as the Bandit King. When he learns about the magic protected by Sister Witch, the Bandit King leads his horde to Ned's village. He plans to steal the magic and hand it over to King Ott of Duunin, knowing the king will pay any price the bandits ask. The Bandit King, already under the thrall of the magic from his pendant, soon realizes he wants all the magic for himself. He leads King Ott back through the Deadly Forest, promising a short battle will defeat the smaller kingdom that includes Ned's village.

In the forest lies a meadow with nine stones standing at attention. The Stones had originally controlled the magic, and they tried to make themselves immortal. It backfired so that they became immortal in rock form. They had taught a family to gather the magic, and guarding the magic has been handed down through generations. It now rests with Sister Witch and Ned. The Stones will be released from their rock forms if the magic is released from this world. Ned, learning that Tam wants his soul to be released as well, commands that the magic be attached to Tam's soul. At the end of the day, Tam's soul, the magic, and the Stones depart, leaving Ned's world to face a new age. A year later, Aine returns to Ned's village. She, the wolf, and her grandmother have been sailing the sea, and Ned is excited to join her.