The story begins with a family of three: Kino, Juana, and Coyotito, who live in the poor side of La Paz, Mexico. Their son, Coyotito, gets stung by a scorpion on his shoulder and is quickly rushed to the doctor. The doctor rejects their pleas for help because of their inability to give anything to the doctor for his service. Kino takes his canoe to the estuary in hope of finding a pearl to pay for their troubles. Luckily, Kino catches a huge pearl and as he catches the pearl, the swelling on Coyotito's shoulder begins to lessen and heal.
The news of the pearl spreads rapidly throughout the town and many people are envious of their luck. The doctor visits Kino to make sure that Coyotito is well but he only does this because of the pearl. The doctor gives Coyotito "medicine" but it makes him feel sick. Days after the doctor's appearance, Kino goes to the pearl buyers to sell his pearl but gets cheated with its value. Angry at the pearl buyers, Kino bravely exclaims that he is going to the capital to get a better selling value there.
Juana has seen the evil the pearl has brought to her family and tries to convince Kino to get rid of the pearl to save their lives. Kino refuses because he believes the pearl is their one shot at having a profitable life and that it will bring happiness for them. One night, Juana sneaks out of the house with the pearl and heads toward the estuary. She gets ready to throw the pearl back where it came from but Kino yanks her away from the water and strikes her for what she was about to do.
As Kino heads back home with the pearl, he gets attacked by a large figure. Kino knows the reason he is getting attacked and believes it is the doctor who wants to make him suffer. The attacker manages to steal the pearl from Kino and reaches for something in his shirt pocket but shortly resumes his attack on Kino. As Kino gets beat and struggles to fight off his attacker, he gets knocked unconscious with a sharp rock. Before he hits the ground, he hears Juana scream and a faint crackling sound. A few moments later, he comes back to consciousness due to Juana violently shaking him awake. Tears streak down her cheeks and onto his face but Kino feels the stench of something burning. He realizes that Juana is screaming at him to get up and her face is crinkled with worry. Kino stands up and sees the source of the crackling noise and the burning smell. The woods is on fire and he can faintly hear his village screaming in terror. For the first time, Kino doubts the blessing of the pearl as he watches his world go up in flames.
A few hours go by until the fire finally calms down. Half of Kino's village is damaged and the woods has been stripped of its beauty. The Song of Evil is deafening in Kino's ears and he solemnly looks at the destruction his attacker has caused. Rage begins to boil in Kino's bloodstream because of the attacker got away with the pearl and destroyed his life. Juana hasn't made a single sound since the village burned to ruins. She has been cradling Coyotito in her arms and looks lost in her own body. Kino tells the whole village that the doctor is the one who attacked him and proceeded to harm him by burning down his home. Everyone believes Kino and plans of an uprising begin to spread throughout the hearts of all those who were affected by the fire. The village begins to gather knifes, pitchforks, and other weapons to attack the doctor for his cruel actions and lack of compassion towards Kino and his people. Juana is still cradling Coyotito when Kino goes to fetch her to get their revenge. Juana tells Kino that she will not go with him because there has been a lot of evil surrounding her soul and her family that she does not want to fuel the fire any longer. Tired of his wife's resistance, kino leads his people to the doctor's home, chanting in angry, blissful tones. When they arrive to the doctor's home, they discover to their astonishment that the doctor has abandoned his home.
Back at the destroyed village, Juana carries Coyotito and places him in a brittle basket when the dark figure stealthy, approaches her. Juana senses someone advancing in her direction and quickly takes out her knife for protection. The dark figure snatches the knife from her but she does not counter his movements because it is Kino's brother, Juan Tomás. Relieved at his presence, she turns a deep shade of red because their plan did not go as they had hoped it would. Juan Tomás was Kino's attacker and was the one responsible for igniting the fire. Juana saw the damage the pearl was going to inflict upon her family and saw the dark road Kino was going down on. No one would listen to her because no one believed that a precious treasure, such as the pearl would ever curse someone. Also, no one believed the word of a woman against the word of a man. The only person who believed Juana was Juan Tomás because of his wise nature and he was not blind to the pearl's evil nature. Juana didn't want Juan to attack Kino in their house where everyone would hear the commotion, so she led Kino to the farthest point of the village. She knew that Kino's life revolved around the pearl and knew that she wouldn't get away with simply throwing the pearl into the deep waters. Juana told Juan that once Kino heads home, he will attack Kino but not dangerously hurt him just so he can snatch the pearl away from him. Juana berated Juan for setting the whole woods and village on fire because that was never the plan. Juan reassures Juana that everything will be fine because the pearl is the root of all evil and the fire was just a little bump in the road to get rid of it. Juan grabs Coyotito and Juana's hand to lead them down to the water. Once they reached the waters, their expressions turn from calm to sad. The once clear and sparkling water was now dark and murky. The waters reflects their lives ever since the pearl entered the palm of Kino's hand. Juan takes out the pearl and without hesitation, launches the pearl into the waters. Juana lets out a joyful cry of relief while Juan faintly smiles at their fortune that all the evil is out of their lives.