The central theme of Kidnapped is the friendship between Alan and David. It is an unlikely pairing: the young, naïve, properly Protestant Whig, David Balfour, and the older, rebellious, adventurous, Catholic Jacobite, Alan Breck Stewart. Stevenson may have wanted to show that the Whigs and the Jacobites could meet eye-to-eye sometimes, and even become friends, despite their bloody history.
Whatever his intention in the match-up, the friendship soon becomes the most significant aspect of Kidnapped. There are several scenes that reveal its centrality. For instance, at one point David and Alan see the warrant for their arrest. David's description is vague and his name is not included, so now that he has changed his clothes, David realizes he can walk freely and not look suspicious—so long as he is not with Alan, who is named and much easier to recognize. David knows it would be safer for both of them to split up, but he never even points this out to Alan. Despite the fact that Alan actually owes him, since David aved his life on the Covenant, David feels a great sense of loyalty to Alan, so he cannot bear to part with him. Even when he becomes angry with Alan for losing their money to Cluny Macpherson, David resists the temptation to leave Alan. Alan, for his part, continues to lead David through the wilderness, even when it is apparent that David is often a hindrance to him.
The climax of the novel occurs in Chapter 24, "The Quarrel," where the friendship reaches it highest point of crisis. David, tired, sick, nursing his anger against Alan for losing their money, and become more and more annoyed with Alan's anti-Whig taunts, finally explodes with a number of vicious verbal attacks on Alan. His words are sharp, and cut Alan just where he knows it will hurt most, on his skill as a fighter. David points out that Alan has been "beaten on both sides" and comments on his loyalty to his clan. In his rage and delirium, David sees no choice but to challenge Alan to a duel, but Alan cannot do it, knowing it is murder. David swiftly realizes what he has done and, knowing no apologies can make up for it, he exaggerates his sickness, claiming that he lies near death, and asking Alan to forgive him. Alan does, saying he is actually impressed now that he knows David can "quarrel," and he takes David to a safe house to become healthy. From there, the two return to Cramond, where Alan helps David recover his inheritance. The book ends with their separation, again revealing the true heart of the novel lies in their friendship.
One of greatest difficulties David has with his travels in the Highlands is understanding its people. David has known a very set ethical code all his life, that of a Protestant Whig. He is used to the concept of solving differences through the use of lawyers and relatively fair trials, and his sense of right and wrong is informed by religious teachers such as Mr. Campbell. In the Highlands, he is exposed to a very different set of ethics.
The Highlanders, particularly Alan, have values that, while similar to David's, often have important differences. Both have a strong sense of justice, but David believes it is settled by finding the most obvious guilty party and punishing him, such as when he suggests that James Stewart put out a warrant for the real killer of Colin Campbell. Alan and James, however, believe that to persecute the real killer would be unjust. To them, vengeance is a code of ethics that is acceptable. Campbell's death is justified by his terrible actions toward the Highlanders in life. Therefore, they will do what they can to protect his killer. David might be willing to agree that Campbell should be punished for his terrible behavior, but he would also agree that the killer should suffer the consequences of his actions.
The growing appreciation that David and Alan begin to have for each other's views is one of the most significant aspects of the novel. Stevenson attempts to portray the Highlanders and their people sympathetically, and to give the reader a glimpse into their behavior, their lives, and the nobility of their own code of ethics, which, though "tail-first" in David's words, are nonetheless very important to them.