The Sea of Lost Sons is a story within a story. It begins with the fictional resumption of Treasure Island shortly after Captain Bones dies, and pirates raid the Benbow Inn. When Jim Hawkins sails away to find Bones' treasure, Jonah, an orphan, takes his place at the Inn. Later, Jonah walks to Bristol to seek his fortune but is waylaid by a press gang and thrown onto a ship sailing to Africa to pick up captives for the slave trade. Jonah is shocked by the crew's cruelty and befriends a young African boy.
When the ship flounders and is attacked by the notorious Bartholomew Roberts, "Black Bart," Jonah is taken aboard as a powder boy. The British Navy scuttles the pirate ship, Royal Fortune, killing Roberts and capturing the crew. Jonah admires the swaggering, complex ship's surgeon, Peter Scudamore, and tries to prevent his hanging, but Scudamore and the crew die at Cape Corso Castle in 1722.