David Balfour's father, a poor cleric in a small village, has died. His mother has since died, so David is now alone in the world. Mr. Campbell, the local minister, gives David a message from his father to a mysterious "Ebenezer Shaw." That is when David discovers he has unknown relatives.

When David finally arrives at the Shaw "mansion" he is appalled. By now he has learned it has an unsavory reputation and the owner is hated by all the neighbors. Despite this, David approaches the dark, partially finished house. His uncle Ebenezer reluctantly welcomes David. After a short time, David realizes there are secrets being kept. Was David's father the true elder brother? Should David himself be the owner of the Shaw money and lands rather than his Uncle?

Before he can discover the truth, he accompanies his uncle on a business trip to the wharf. They visit one of the ships Ebenezer Shaw deals with. David is coshed on the head and wakes up in the hold, the ship under way. He is on his way to the American colonies to work on the Carolina plantations. At first he is held prisoner; later he is able to work on the ship and have more freedom.

David's adventures are only beginning. As the ship is sailing north around Scotland, they strike another boat and rescue the survivor. This survivor has secrets, connections, and money. Quickly David finds himself aligned with this man against the sailors. From there he encounters hardships, travails, and excitement he could not have imagined before he left his father's home.