After the death of his parents, 17-year-old David Balfour sets out to make his way in the world. Arriving at his family estate, David is confronted by his uncle Ebenezer, who is jealous of his nephew's inheritance. Ebenezer leads David to a visiting ship, where he is struck, bound, and kidnapped. This leads David on a journey that includes being stuck on a desert island, an attempted stabbing, and being accused of murder, while trying to regain his family fortune.

Kidnapped is set around real 18th-century Scottish events, notably the "Appin murder", which occurred in the aftermath of the Jacobite rising of 1745. Many of the characters are real people, including one of the principals, Alan Breck Stewart. The political situation of the time is portrayed from multiple viewpoints, and the Scottish Highlanders are treated sympathetically. The novel raises various moral issues, such as the nature of justice and the fact that friends may have different political viewpoints.