Kino and Juana travel through the night and when dawn approaches find a concealed place to rest in the bush. They hide the next day before setting out for the capital at night. The family takes refuge with Kino's brother Juan Tomas and Juan's wife, Apolonia. Kino then finds that his canoe has been vandalized, their house has been searched, and the flimsy structure has been set on fire. Juana finds the pearl on the path, and the couple decides they must leave, even though the killing was in self-defense, as they will not get a fair hearing. A thief whose throat Kino has slit lies dead in the bush. Juana watches from a distance and then sees Kino approaching her, limping.
A group of men accosts Kino and knocks the pearl from his hand. Later that night, Juana attempts to take the pearl and throw it into the ocean, but Kino finds her and beats her for doing so.
However, Kino vows that he will not be cheated. That night, Kino is attacked by more thieves, and Juana once again reminds him that the pearl is evil. Kino refuses to sell to the pearl dealers and decides to go to the capital instead. They offer Kino a thousand pesos for the pearl, which Kino believes is worth fifty thousand. The dealers are aware through the gossip of the town that a big pearl has been found and have agreed to pretend it is a freak and worthless. The dealers are employed to make it appear as though the prices offered are competitive when, in fact, they are kept very low, and the natives are cheated. Unbeknownst to him and all the pearl fishers, the pearl dealers in La Paz are all employees of a single buying organization. The next day, Kino goes to sell his pearl. Juana warns Kino that the pearl will destroy them, but Kino insists that the pearl is their one chance for a better life, and that tomorrow they will sell it. That night, a thief attempts to break into Kino's hut, but Kino drives him away. (Kino had buried it in the corner of his hut.) Kino tells the doctor that he will pay him once he sells his pearl, and the doctor attempts to discern where the pearl is located. The doctor also visits, and although Coyotito seems to be healing, the doctor insists that Coyotito still faces danger and treats him. The local priest, hearing the news, visits and tells Kino to remember to give thanks and to pray for guidance. He claims that he will send Coyotito to school and buy a rifle for himself. Juan Tomas, Kino's brother, asks him what he will do with his money, and Kino envisions marrying Juana in a church, and dressing Coyotito in a yachting cap and sailor suit. Kino's neighbors begin to feel bitter toward him for his good fortune, but neither Kino nor Juana realizes this feeling that they have engendered. The news that Kino has found an immense pearl travels swiftly through the town of La Paz. He finds a very large oyster which yields an immense pearl, and which he dubs "The Pearl of the World". Kino dives for oysters from his canoe, hoping to find a pearl he can sell to pay the doctor. Kino and Juana take Coyotito down near the sea, where Juana uses a seaweed poultice on Coyotito's shoulder, which is now swollen. Juana and Kino, accompanied by their neighbors, go to see the local doctor, who refuses to treat Coyotito because Kino cannot pay enough to sustain the greedy doctor's lifestyle, and because the doctor holds racist views towards the poor Amerindians. Although Kino kills the scorpion, it stings Coyotito. Kino attempts to catch the scorpion, but Coyotito bumps the rope, and the scorpion falls onto him. Kino watches as Coyotito sleeps, but sees a scorpion crawl down the rope that holds the hanging box where Coyotito sleeps.
The Pearl, which takes place in La Paz, Baja California Sur, begins with a description of the seemingly ideal family life of the poor pearl fisherman Kino, his wife Juana, and their infant son, Coyotito.