A continuation to the previous book Flowers in the Attic, the story starts off with Cathy, Chris, and Carrie using their stolen funds to escape by bus to Sarasota. Carrie, still weak from the effects of the poison that killed her twin, is taken ill on the journey. While her elder siblings panic over how to get her the medical attention she so desperately needs without revealing their identities or exhausting their limited funds, the children are discovered by Henrietta "Henny" Beech, the mute housekeeper of a local doctor, Paul Sheffield. Cathy tells Paul their story and he convinces them to stay with him.
Carrie, though physically stunted through malnutrition and lack of sunlight and fresh air during her formative years, thrives under Dr. Paul's care. The doctor also sees Chris's potential and enrolls the boy into a medical school, where he soon readjusts to life outside Foxworth Hall. Cathy grows to be a beautiful young lady but is still bitter and bent on revenge against her mother, seeing her as the root of every problem in their lives - from Carrie's deformities to Chris's incestuous obsession with Cathy. She is determined to become a world famous ballerina, just as she planned as a child, so that her mother cannot deny her existence.
Though Cathy soon falls in love with Paul, she marries a man in her dance troupe, a fiery dancer named Julian Marquet who has been pursuing her from the moment he saw her. Julian is possessive of Cathy and jealous of her relationship with both Paul and Chris. He abuses her, breaking her toes so that she cannot perform. However, Cathy is pregnant with his child and feels she cannot leave her husband, even though both Paul and Chris insist that she must for her own safety. In the midst of this conflict, Julian is rendered paralyzed in a car accident. He commits suicide in his hospital bed when he learns he will never dance again. Cathy, though guilt-ridden, is free.
After the birth of her son named Jory (J for Julian, the rest for Cory), Cathy once more becomes determined to destroy her mother's life. Under the guise of collecting Julian's insurance, she hires her mother's husband, Bart Winslow, as her lawyer, with the intention of seducing him; however, the two fall in love and begin a prolonged affair. All the while Cathy intends on revealing her true identity as Bart's stepdaughter.
Carrie meanwhile, always depressed over not having a love of her own while Cathy has several, meets a young man and they have a rich courtship. However, when the man tells Carrie he plans to be a minister, it's revealed that Carrie heard and now understood the bitter lectures their Grandmother, Olivia, spoke of, calling the children devil's spawn and sinful. Fearful of being a minister's wife, Carrie is sent into doubt. During this time, Carrie has a chance encounter with her mother. Her mother denies knowing Carrie. This, combined with her feelings that she'll never find love, Carrie commits suicide, leaving a note explaining her reasons. Carrie believed her grandmother about being the "devil's spawn." Cathy becomes even more enraged and vows revenge. She becomes pregnant with Bart's child, an act she believes will be a crushing blow to her mother, who, according to her grandfather's will, must forfeit her vast inheritance should she ever bear children. Bart is torn between his duty to his wife versus his desire to be a father.
Cathy returns to Foxworth Hall and visits the room that she and her siblings were locked up in; She describes the room as being as they have never left. She believes that she heard the voices of Cory and Carrie begging to go outside. Cathy also discovers an unnoticed room in the attic that gives off a musty, rotted smell - indicating that Cory's remains were stashed there. Then Cathy takes her revenge on her mother by exposing the truth to Bart and a crowd of guests at her mother's Christmas Party at Foxworth Hall. The mother confesses in front of Bart but then exposes her side of the story, claiming to be a victim of her father, whose vicious plot was to ensure his grandchildren died trapped in the attic. However, Cathy is reluctant to believe her mother's portrayal of having been a victim rather than a villain. Cathy's mother suffers a mental breakdown in which she suddenly believes that Cathy is twelve again and has somehow escaped the attic to confront her. In her madness, she sets fire to Foxworth Hall. Cathy and her mother escape, but Bart rushes back into the burning house to rescue his wife's elderly mother, who is paralyzed and confined to a hospital bed. Both he and the elderly woman perish. Cathy's mother is committed to a mental institution. In a twist of fate, although she forfeited her father's inheritance when it was revealed she had borne children to her first husband, all that money reverted to her now-dead mother, who stated in her will that her daughter was to receive everything.
Cathy finally marries Paul, but due to complications from a heart attack, Paul dies. On his deathbed, Paul encourages Cathy to be with her brother Chris, who has loved her and waited for her all these years. Cathy is amazed that Chris still loves her and that he wants to be with her, noting that all the men she has loved have died. Cathy and Chris take the name "Sheffield" and plan to raise Cathy's two sons together, although Cathy secretly dreads what will happen to the children if their secret is ever revealed.