The main theme is that virtue and courage will eventually prevail over deceit and evil. To delve into this concept, Stevenson uses the traditional quest narrative. At the urging of his malicious uncle, David is kidnapped and meets Alan, embarking on an extensive journey that involves battles and even taking lives.

Another recurring theme is Stevenson's belief in the inherent duality within each person, highlighting how individuals embody both positive and negative traits. This concept is illustrated through several characters aboard the ship where David is held. The second officer, Riach, demonstrates kindness towards David, but only when intoxicated; when sober, he often behaves cruelly. In contrast, Mr. Shuan is gentle when sober but turns violent under the influence of alcohol, as shown when he kills the cabin boy in a drunken rage.

Even Alan Breck, known for his boldness and aggressive nature, has moments of compassion. During a heated argument with David, when David challenges Alan to a sword fight, Alan hesitates and refuses, saying "it would be murther," acknowledging his superior skill with a sword and David's lack of combat experience.

To sum up, the central takeaway from the novel is the significance of understanding and following a sound moral compass. David begins his adventure as a compassionate boy and transforms into a more mature young man. He gains a deeper comprehension of both himself and the world, alongside a greater appreciation for honesty, bravery, and responsibility.