Chapter four of the pearl ends with late night attack which leaves Kino bruised and battered, but determined to set out for the capital as soon as dawn begins. Although Juana had agreed that she would go with Kino to the capital to sell the pearl, when he hears a shuffling noise in the night he opens his eyes and watches as Juana stealthily unburies the pearl, and slips out the door. Enraged, Kino follows her into the night. Kino is able to catch her just as she begins to throw the pearl back into the ocean. He takes the pearl from her, and in a fury begins hitting her about the face, and kicking her in the sides. Juana falls to the sand, and the sea licks at her crumpled body. She looks at her husband in acute terror, but bares his teeth and hisses at her. Kino is outraged at Juana, and disgusted by himself, but even still he makes no effort to assist her. He simply walks away Kino has become unrecognizable from the gentle man that he was when he discovered the pearl.

As Kino attempts to flee the scene of his crime a new calamity starts up. Hordes of men rush him, and he is able to stab one of them, but they continue to assault him, feeling around his body for the pearl. The force of the attack causes Kino to drop the pearl. Simultaneously, Juana is has freed herself from the rocky shore and is stumbling up the beach. In her heart, she has forgiven Kino. Because he is a man she sees him as "half insane and half god." She forgives him his flaws, because she has determined that she needs him. As she is making her way back home Juana sees the pearl on the ground, when she bends to pick it up she notices two bodies in the road, she realizes the one of them is Kino, and the other is a man that he has killed. Juana is horrified, and realizes that life she had been trying to salvage by discarding the pearl was gone forever. She decides that the only thing she can do is save her family, so she drags the dead man into the bushes.

When she begins attending to Kino his only thought is for the pearl, which he says he has lost. Juana consoles him, explaining that she has found the pearl, but also informs him that he has killed a man, and that the family must now flee. Kino justifies his action as self-defense, but Juana protests that nobody will care about his explanation. Kino concedes that his wife is right, and tells her to go get the baby and as much corn as they had, so that they can flee in the canoe.

As Juana rushes back to the brush house, Kino heads to the shore to get the canoe ready for their journey. When he reaches it, however, he finds it in ruins. Somebody has cut the bottom out. Worried for the safety of his family, he makes his way to the brush house, which he finds ablaze. Shortly after he sports the burning house he is met by Juana who is holding Coyotito, she confirms that house was ransacked and burned. The village is in complete chaos, because the brush houses can easily catch fire. Nervous, Kino and his family duck into his brother's house unnoticed. They listen to the people outside speculate that the entire family has died in the blaze. Juan's wife Apolonia is particularly inconsolable.

When Apolonia returns to her home Kino whispers to her to stay quiet about their presence and survival. Juan also agrees when he returns a few moments after Apolonia, and he allows the family to pass the night there. In the morning speculation continues about what happened to Kino and his family, with most agree that they have died. However, Juan suggests that they may have fled south along the coast to save themselves from the persecution they have experienced since finding the pearl. That night the family leaves their village heading to the northern cities to hopefully, finally, rid themselves of the pearl that has caused them so much pain. They are hopeful that the ideal weather conditions and the misleading statements Juan made will prevent any trackers from catching up with them.

Kino and his family walk for hours and hours through the night without being seen by, or seeing another human being; what they do hear was wild animals, many of them threateningly close. At dawn the family finally stops to rest in a ditch by the road. Soon, an oxen and cart passes by them, fortunately, its driver doesn't notice the family. Junana and Coyotito slept, but Kino could not. When Juana awakes it was extremely hot and dry. She asked Kino if he thought that anyone would peruse them, and he said he knows that they will. At this point Juana confesses that she thinks the pearl dealers in town might have been right: that the pearl is of very little value. Kino points out that the family would not have been terrorized if the pearl was indeed useless.

Kino again looks into the pearl in an effort to see his future. He tells Juana that when they sell it he will have a rifle, Coyotito will go to school, and they will be married in a church. However, he is lying. What he actually sees is his family in its entirety dead or mutilated.

Later, Kino is finally able to sleep, but awakes suddenly when he feels something is amiss. He leaves his family to investigate and finds trackers inspecting the road they had been on. It looks as though the men will find the family, but eventually they were confused by the trail, and started in the wrong direction. He scrambled back to Juana and the baby, and urged them to come with him. But suddenly, Kino gives up and declares that maybe he should "let the trackers take me." Juana is infuriated, and forces him to move on.

The family fled quickly up hill, and through the desert without any water. Eventually Kino realizes that the trackers will catch up to him, and suggests that he will lead them on, so that she can take refuge in a nearby village with the baby. However, Juana refused and they continue on for hours zigzagging through the desert with dim hopes that the erratic pattern might throw off the trackers. Eventually the dehydrated family found a spring, and a cave where Juana and Coyotito hid in hoped that the trackers would pass them by. Unfortunately, the three trackers decide to camp close to the cave. When two of them fall asleep, Kino hatches a plan to slit the throat of the man keeping watch.

Kino made his way to the tracker's camp, and was just about to attack the watchmen, when Coyotito begins whimpering from the cave. It wakes all of the trackers up, and they proceeded to speculate about what it is, one thinks it is a human infant, another a baby coyote. One man gets up and fires his rifle in an effort to quiet whatever is making the noise. Kino leaps for the man, and slits his throat. Now in possession of the weapon Kino strikes one tracker with it, and shoots the remaining man. When all is said and done it is eerily quiet.

And then Juana shrieks. The trackers bullet had found its mark in Coyotito, and the little boy was dead.

In shock the couple return to their own village with Coyotito dead in a sack across his fathers back. They walk silently through the town, and then their little village, and down to the ocean, where they toss the pearl in the roiling blue.