The initial portion of the plot focuses respectively on the families of the foremost major characters before they end up interacting with each other. The story begins in Salinas Valley, California and is recounted by the narrator who proclaims himself a relative of the Hamilton family. His Irish ancestor, Samuel Hamilton, settled in Salinas Valley with his wife, Liza, and eventually became parents to nine children. Salinas is also where Samuel Hamilton met Adam Trask and his pregnant wife, Cathy, who relocates from Connecticut in search of a new life for his growing family.
Adam is the son of Cyrus Trask, a deeply crooked character who made his wealth dishonorably during his time as an administrator in the US Army. He is able to leave a fortune of $100,000 to his sons, Adam and Charles, brothers who were poles apart in their personalities; Adam is mild-mannered while Charles is the quick-tempered and moody one. The two brothers have always been unable to get along due to Cyrus’s very apparent favoritism towards Adam. As a result, Charles has always resented his half-brother, even after the demise of their father. The Trask brothers reach their final drift with the arrival of Cathy, a girl in near-death condition who wanders near Adam’s farm after being suspiciously beaten severely by her assailant. Charles is immediately suspicious of the girl and advises Adam to get rid of her immediately but the good-natured Adam takes in Cathy and resolves to restore her to perfect health. Despite Cathy’s silence regarding her part, he is quick to accept her and asks her to marry him, to Charles’s utmost disapproval.
Cathy is quick to accept Adam’s proposal as she realizes that this is her best opportunity for survival at that time. Her assailant was Mr. Edwards, the proprietor of a number of brothels who takes in Cathy as his own personal mistress after she comes to him for work under mysterious circumstances as she refuses to even disclose her last name to him. Her last name is Ames and she has been under hiding after having killed her parents by setting their home on fire and she stole all their money. After an incident with Mr. Edwards who realizes her true nature and her previous sins, he beats her and leaves her to die, only to be rescued by the Trasks. Cathy and Adam get married; on their wedding night, she drugs her new husband and takes Charles to bed, leaving the readers to wonder about the true paternity of her soon-to-be-born twin sons.
Soon after the marriage, Adam moves to Salinas Valley with Cathy and therefore meets the Hamilton family. He employs a Chinese-American named Lee to take care of the house and builds up a friendship with Samuel. Meanwhile, Cathy struggles with her pregnancy and to Adam’s ignorance, even once attempts to abort the child. The Hamiltons and Lee are both wary of Adam’s wife and are able to somewhat sense the darkness in her. Cathy waits till the birth of her sons, Aron and Cal, and then leaves her husband and family. When Adam tries to stop her, she puts a bullet through his leg.
Adam decides to hide the truth of his injury from the sheriff by covering up the gunshot wound as an accident. He raises his sons with the help of Lee and gradually, as time passes, they grow older, forming part of the next generation. Aron takes after his quiet and mild-mannered father while Cal resembles his mother in nature, ruthless and calculative. It is as if history had repeated itself by incarnating the two sons in the nature of their father and half-uncle, Adam and Caleb. However, Cal is less like Charles in the sense that he struggles to move away from the dark side of his personality, praying to God to make him more like his brother. He also secretly resents his father for favoring Aron over him, as Charles had resented Cyrus many years ago, and realizes that it is because of his brother’s striking resemblance to their mother. Even after Cathy’s blunt betrayal, Adam is unable to forget her and suffers quietly from heartbreak, not unnoticed by Samuel, who is aware of Cathy’s ventures after the departure from the Trask family.
After leaving Adam, Cathy takes refuge in a local brothel, gradually winning the trust of the madam, Faye. Faye is manipulated by Cathy’s quiet grace and passive nature, and she soon adopts her as a daughter, even resolving to put her name in the will. After having convinced everybody of her deception, Cathy puts her latest plan to work. She slowly starts to poison Faye and kills her, taking control of the house. Cathy changes the rules of the brothel and the clients as well, serving highly influential men and keeping secret photographs of their sadomasochistic acts as leverage against them. Samuel informs Adam of his wife’s activities, hoping to jerk him out of his listlessness. Soon afterward, Samuel passes away.
After his dear friend’s demise, Adam reaches out to his wife after these several years of separation. He is shocked at her drastic change in appearance as now Cathy truly looked like the shrewd and cunning sociopath she truly is. After his encounter with her, Adam is finally able to see her for who she truly is and move on from the love he had for the version of her he believed he had married. He becomes more actively engaged in his sons’ lives and moves the family into the town so that Aron and Cal can have a better education. This is when the brothers meet Abra Bacon, the daughter of the county supervisor and both fall in love with her, although Cal is less reciprocating about his feelings as he secretly doubts himself of being worthy of Abra.
More time passes and now Cal has become even more self-destructive and takes to visiting brothels in order to keep him from thinking about Abra and Aron’s budding romance. He learns of his mother’s profession and recognizes her familiar face, the one similar to his brother. Nevertheless, he keeps this news to himself, realizing what it would do to Aron if he were to be made aware of this information. Internally, he is also emotionally battled as he suspects that the cruelty in him is inherited, something he fears that his mother has passed onto him and cannot be truly eradicated from his soul.
As one brother questions the presence of sin and evil, the other abhors even the idea of it. Aron turns to religion in order to protect himself from the cruelty and dishonesty in the world while Cal tries to fight the evil he believes already exists in his heart. Aron’s lack of human communication builds a distance between him and Abra, who discovers that Aron’s attraction towards her is harnessed by his belief of her apparent perfection. She finds herself more drawn towards Cal, more so as Aron graduates from school and departs for Stanford University.
Meanwhile, Adam tries his hand in business but manages to waste most of his wealth on a loss. Seeing this as an opportunity to gain his father’s favor, Cal tries to recover the money his father lost by investing in a business that put to use the hard work of farmers forced to sell at a lower profit due to the struggles of the First World War. Adam is surprised when Cal gifts him the profit but enraged when he hears where the money has come from. He is harsh with his son and once again, Cal is reminded of his father’s disapproval. In his rage, he decides to take it out on his brother and takes him to see their mother on his trip back home. The encounter proves to be destructive for both mother and son; Aron is horrified to learn that his mother, who he considered to be dead, is the madam of a brothel and Cathy is overwhelmed as well at Aron’s disgusted reaction at meeting her. Quite soon afterwards, Cathy commits suicide by overdosing on morphine, leaving behind her entire fortune to Aron, who has run off to join the army.
Adam learns of his son’s action and transforms into a state of shock. Cal is wretched with guilt and blames himself for the turn of events, despite Lee and Abra’s continual efforts to remove him from his state of guilt. Lee understands Cal’s perils and tries to convince him that no one is truly evil and that the human being is a flawed machine that is prone to making mistakes.
A message arrives home carrying news of Aron’s death and Adam has a stroke. Before Adam succumbs to his illness, Lee brings Cal to his father and successfully reunites the father and son pair. Adam finally realizes that all of Cal’s actions were to procure his father’s love. He blesses Cal and Abra and takes his leave from the world, whispering one last word, “timshel”.