David awakens in the brig of the Covenant, in pain and bound by ropes on his hands and feet. He is suffering from seasickness as well, and each lurch of the ship brings a fresh batch of pains. Several days and nights pass as David wanders in and out of consciousness and he is beginning to get a fever. A man visits David briefly, gives him some brandy and water, and dresses his scalp wound. Then he is left in darkness again, and the rats scurry over his face.
Mr. Riach, the ship's second officer, brings Captain Hoseason down into David's room to show the captain how poorly the young man is doing. Hoseason is unsympathetic, and seems inclined to leave the boy to rot and die, but Riach asks to move David to the healthier area of the forecastle, with the other sailors. When the captain refuses, Riach accuses him of being a party to murder, and the captain relents.
David rests in the forecastle for several days as Riach nurses him back to health. He comes to know the sailors, who he finds less rough than he did before. They even give him some of his money back. Ransome often visits him, always with a new wound from Mr. Shuan.
David tells Riach the story of his uncle and how he came to the Covenant, and Riach claims he will send a letter to David's father's lawyer, Mr. Rankeillor, as well as Mr. Campbell, if he gets the chance.
Ransome is brought into the forecastle; Mr. Shuan has killed him. Hoseason orders David to become the new cabin boy. He sends him to the Round-House, the officers' cabin. Shuan is a wreck; killing the boy has ruined his already tenuous sanity.
David becomes used to his duties, and finds it not so bad a life. Riach does not abuse David, his wits being gone. David tries to speak to Riach and the captain about their plans for him, and his plight, but they won't listen, and David has visions of himself slaving in the colonies of North America.
The Covenant strikes another boat, a much smaller one. Upon checking they find a single survivor, a man dressed in fine French clothes and carrying a pair of pistols and a long sword. He speaks with a Scottish accent. He is a Jacobite, a man who believes that the Stuart line, of which King James I and his heirs, are the true kings of England, and should be restored to the throne. Being a Jacobite also means the man is a Catholic, but the captain is a Protestant. Nonetheless, the captain is interested in helping the man in exchange for his gold.
The man asks the captain to set him down in France, where he was heading, but the captain refuses. So the man asks to be set down somewhere in Scotland, and they begin to discuss terms. They come to an agreement, and the captain excuses himself and his officers.
David takes a liking to the stranger, and overhears the captain and officers plotting to murder him and take his money belt. David runs back and tells the stranger, then agrees to fight by his side. They introduce themselves; the stranger is Alan Breck Stewart. The two men prepare to battle the captain and his officers. Fortunately, the Round-House contains all the pistols and other weapons. Alan prepares to guard the front with his sword, while David loads all the pistols and covers the back door and the skylight.
The adventure begins in earnest in these chapters, as David is separated from everything familiar—Mr. Campbell, the Lowlands, even wicked old Ebenezer—and shipped out into the middle of nowhere. The realism found in these chapters, at least until the appearance of Alan Breck Stewart, is a bit surprising for a story intended for younger readers. David does not find himself in the company of decent sailors as well as cutthroats, as Jim Hawkins does in Treasure Island, but only greedy merchants who do not mind selling men into slavery.
Moreover, David does not have his wits about him to work against the rough sailors. Instead he gets a fever as rats scurry over his face. He nearly dies in the fetid cargo hold, and few of the sailors have any sympathy for him. But the most horrific detail is the death of poor Ransome. After Stevenson shows that Ransome is a silly, misguided, but good-hearted boy, he is cruelly murdered by the drunk Mr. Shuan. The sight of the boy's pale, wax-like face, with a "dreadful smile" upon it, is probably the most horrible image in the whole book. But what makes it so terrible is the reader's familiarity with Ransome. There is death in Treasure Island, but is never this personal for the reader.
But once Ransome is gone, the story resumes a more "normal," adventurous tone. David has passed through a sort of trial, by surviving the sickness and then managing to manage his anger against his captors enough to serve them as a cabin boy. The next trial will be one by fire, as David helps Alan Breck Stewart defend himself against the men of the ship.
In their brief dialogues in these chapters, David and Alan begin the dynamics that will serve as the primary hinges of their relationship. The first, and most significant, is their religious and political affiliations—Alan is a Catholic Jacobite, and David is a Protestant Whig. A Whig was a supporter of the English government, who tried to suppress their Jacobites and their claims that the Stuarts belonged on the English throne.
Another dynamic is the question of status. David feels compelled to introduce himself as "David Balfour of Shaws," indicating his upper class status. While Alan believes David, he also feels it necessary to mention that his own name is shared with a king. For most of the novel, David's "gentleman" status will balance out with Alan's greater age and worldly experience, though in the chapter twenty-four, "The Quarrel," they will argue over some of these issues.
Finally, this chapter reveals Alan's competence, a trait often hidden by his arrogance and his flamboyant behavior. He is an experienced fighter, and David is not at all. The ensuing battle is the only real battle in the entire novel, and in it David will deal his first wounds to another man, and ultimately cause their death.