Kidnapped tells the story of David Balfour, a young man of the Lowlands, the southern part of Scotland. David's father, Alexander Balfour, has recently died, and his mother died some time before, so he is now an orphan. Since he is now seventeen years old, he has decided it is time to go and seek his fortune. Before he leaves for the city of Edinburgh, he meets with his guardian, Mr. Campbell. Campbell reveals that David has an uncle, Ebenezer Balfour, of the House of Shaws—meaning that David is, to his surprise, from a wealthy family. David decides to go to Cramond, where his uncle lives, and meet his wealthy relatives.

David walks two days to Edinburgh, and soon finds his way to Cramond. As he begins to ask about the House of Shaws, he finds it is an unpopular place. His Uncle Ebenezer seems particularly ill regarded by the community, and is in fact the only occupant of the house. Nevertheless, David continues on to the House of Shaws. Ebenezer gives him a cold welcome, and seems very interested in the death of David's father. Ebenezer treats David badly, almost as if David were a thief, but he wins some of David's respect by giving the lad nearly forty pounds. But when Ebenezer nearly sends David to his death in the tower adjacent to the house, David demands to know why his uncle hates him and, if he does, why he wants him to stay at the House of Shaws.

A cabin boy, Ransome, arrives at the House of Shaws. He has been sent by Captain Hoseason of the Covenant, a ship that deals with some of Ebenezer's financial ventures. Hoseason has requested to see Ebenezer, so the old man decides to go to the port of Queensferry with Ransome and David. David is interested in seeing the ships at the port, so he willingly goes along. At first, Hoseason seems very pleasant. He even warns David that Ebenezer means mischief toward him. Hoseason then asks to speak to David on the boat, and David agrees, being interested in seeing more of the boat. Once he is on, however, the boat swiftly departs, and as he screams at the dock for help, the sailors knock David unconscious.

He awakes in the dark storage deck of the Covenant. As he drifts in and out of sleep, he quickly becomes ill, and soon he is lingering near death. The ship's mate, Riach, demands that the boy be allowed to sleep in the healthier forecastle of the ship with the other sailors. Hoseason reluctantly agrees, and as David recovers he becomes friends with Riach and a few of the other sailors. Then, Ransome is accidentally killed by Mr. Shuan, and David becomes the new cabin boy.

After a few days at this new job, the Covenant strikes and sinks another boat. One man survives, a strange Highland man dressed in the clothing of a French soldier. The stranger tells the captain that he is carrying the rent money for his disenfranchised chieftain. The two men make an agreement that Hoseason will drop the stranger off in Linnhe Loch, but no sooner is the captain gone from the Round-House—the officers' lounge where the visiting stranger is kept—when David overhears the officers plotting to murder the stranger and take his belt. David tells this to the stranger, and agrees to fight by his side. The stranger says his name is Alan Breck Stewart. Alan and David successfully defend the Round-House from the sailors, Alan killing several men and even David taking two himself. Alan, impressed with David's courage, gives David a silver button from his coat. The captain and Alan negotiate, and the captain agrees to drop Alan and David off near Linnhe Loch.

On the way, however, the ship strikes the Torran Rocks and goes down. David escapes and finds himself on an island. The island is separated from a larger main island only by a river, but he can find no way to cross the river. After a few days, a fisherman comes in a boat and reveals to him that the river gets very low at high tide, and David crosses easily.

David then stays at a house, and discovers that Alan himself passed through, having survived the wreck. Alan left instructions that David should follow him to Torosay, and from there go to Alan's homeland of Appin. David heads this way, meeting several disreputable people along the way, including a notorious blind robber; but the young man manages to avoid any great dangers. He meets a pleasant old religious instructor, Henderland, who helps David secure a boat to take him to Appin.

As soon as David arrives in Appin, he comes across a group of four men on horseback. One of the men is Colin Campbell, the King's Regent for that area, whose clan, the Campbells, are hated by Alan and his Stewart clan. As David speaks with Campbell, he is suddenly shot and killed by an unknown assailant. One of the people in Campbell's party accuses David of distracting Campbell so that he could be shot, and just as soldiers are about to apprehend David he is pulled away by Alan, who has been fishing nearby.

Alan and David, now major suspects in the murder, flee to the woods. Alan swears he had nothing to do with the murder, but he must now draw attention away from the real killer. David believes Alan, and they escape to the home of James Stewart, or James of the Glens. James gives them a change of clothes and some little money, but he tells them that he will have to blame them for the murder and put our warrants for their arrest once they are safely gone, so that he will not be blamed for the murder. If James is killed, it will mean great difficulties for the Stewart clan. David and Alan agree to be the scapegoats, and Alan and David are soon fleeing through the wilderness once more.

They hide for a whole day on top of a large rock while English soldiers roam around below, searching for them. They escape and go to a mountain where they rest for several days and send word to James, hoping to get a little more money so that Alan can escape to France. The messenger returns with a note from James' wife; James has been arrested for the murder. She also sends a little more money for David and Alan.

The two continue on their flight, soon reaching the broad, flat region known as the moors. They take some time out to rest, but David oversleeps on his watch, and a troop of English soldiers nearly takes them by surprise. They must run through the wide, flat land on their hands and knees, hiding in small brush and behind rocks. They manage to escape and are ambushed by Highland men who, fortunately, turn out to be men of Cluny Macpherson, another disenfranchised Highland leader. Cluny takes them in his hideout in the mountain of Ben Alder, and while David sleeps for nearly three days, Alan and Cluny play cards. Alan gambles away all their money, including David's. Cluny agrees to give them their money back, plus more, but Cluny is mortified that they thought he would keep the money, David is angry that Alan gambled it away and he has to swallow his pride and ask for it back, and Alan feels guilty for having gambled it all away.

Alan and David continue on their journey toward the Lowlands, but David is now angry and bitter toward Alan. Alan feels remorseful for some time, but when David refuses to warm up at all, Alan thinks that he has personally suffered enough, and soon becomes his usual happy self, taunting David for being a Whig. Alan is a Jacobite, someone who believed the Stuarts, a Highland clan, should be on the throne, whereas Whigs were supporters of the current English monarchy, following the line of William and Mary. David's patience wears thin, and he viciously attacks Alan's honor. Realizing he cannot be forgiven for what he said, David pretends that he is about to die of exhaustion, and Alan becomes very worried and takes David to a house.

Over the course of a month, David recovers. There is some brief trouble when Alan meets Robin Oig, one of the sons of the well-known Highlander Rob Roy Macgregor, who was also a Campbell. But instead of using guns, they duel by playing the bagpipes, and the two men quickly respect one another and a crisis is averted.

David and Alan finally move on and, after some difficulties, reach Queensferry once more. They cross over and David meets with his family's lawyer, Mr. Rankeillor. Rankeillor believes his story, but David's uncle Ebenezer must be dealt with somehow. It turns out that Ebenezer and David's father had had a dispute over a woman, David's mother. They had finally come to an agreement—David's father married his mother, and Ebenezer took the estate and the Balfour fortune, although he was not the elder brother. Rankeillor says the agreement is not legally binding, and that David is the true heir of the estate. But David does not want the House of Shaws, just a pension from its yearly earnings.

To rectify the situation, David plays a trick on Ebenezer. Rankeillor, David, and Alan go to the House of Shaws. Alan walks up to the door alone, and pretends that he is from a bunch of Highlanders who found David alive shortly after the shipwreck on the Torran Rocks. He asks for money to return to the boy, but Ebenezer refuses to pay anything. Alan then says that they'll kill him unless Ebenezer pays to have him kept alive. Ebenezer does not want the boy dead, and as he haggles over how much he will pay he admits that the plan had been for Hoseason to sell the boy into slavery in the Carolinas. At that point, David and Rankeillor reveal themselves, having caught Ebenezer in the confession. Ebenezer and Rankeillor then work out an agreement that David would get two-thirds of the yearly income of the House of Shaws.

David receives a note from Rankeillor that will allow him to collect his money. David then speaks to Alan, and arranges to send him money so that Alan can get passage to France. The two men part, and David wanders into town to claim his fortune.