The story begins when Margaret Lea, an amateur biographer, is invited to the home of Vida Winter in order to record her biography before the famous and mysterious novelist succumbs to her terminal illness. Lea is surprised by the offer and decides to read Winter's Thirteen Tales of Change and Desperation, in which there are actually only twelve tales. Curious, Lea decides to meet with Winter, and at least decline the offer in person. During their meeting, Lea is convinced to change her mind and accept the offer when Winter promises her a ghost story that involves twin girls. Winter's pleas and promises help to draw Lea in, and by the end of the meeting they've come to an agreement. Winter provides her with three truths that can be verified and in turn Lea agrees to hear her story.
Vida Winter's story is an adventure into her own past, full of dark family secrets which she has kept hidden all of her life. She speaks of her childhood and the estate she grew up on, Angelfield, which long ago was burned and abandoned. She reveals that she was formerly known as Adeline March, and tells the tale of the twins, Adeline and Emmeline. The twins' lives are surrounded by dark mysteries involving strange deaths, obsessive loves, incest, and of course, the ghost. Over the course of their lives, the twins are repeatedly abandoned and neglected, their care left to those outside of the strange and seemingly doomed Angelfield family.
It begins with Isabelle and Charlie Angelfield, the children of a wealthy but apparently eccentric man. After his wife's death, Isabelle becomes the obsession of her father, who dotes on her and ignores his son. In adulthood, she forms a bond with her brother that borders on incestuous, but eventually runs away to marry another man. Her father is so devastated that he succumbs to illness and dies. Isabelle later returns to the estate with her twin daughters and is welcomed back by her brother. The two are so enraptured with each other that responsibility for the twins soon falls to the housekeeper. As they grow older, they become increasingly unruly, to the point that a local doctor becomes involved. After a violent incident, Isabelle is sent to an asylum, leaving Charlie in despair. Eventually, Winter reveals she found his body, though the inhabitants of the estate had assumed he'd disappeared and kept his disappearance a secret for years.
Winter allows no questions as Lea records and becomes more and more enraptured with the story. During the present time period, Lea also explores the ruins Angelfield estate, befriends the caretaker, Aurelius, and deals with finding out that she also had a twin. Through her own research, Lea discovers that one of the twins, Emmeline, had lived in the house with Miss Winter, and that there had been a third girl at Angelfield. Miss Winter confirms these facts and reveals that she was not Adeline, but rather this third child. She had grown up there mostly in secret, as the daughter of the disturbed Charlie Angelfield. In adulthood, Adeline had attempted to kill her twin's baby. Winter had saved the child (who grows up to be Aurelius) and returned to the house to find it burning, before saving Emmeline as well. After the fire, she is mistaken for Adeline (who perished in the fire), and never corrects the mistake.
By the end, both of the women are forced to deal with their troubled pasts and the burden of family secrets. Only at the conclusion is Lea finally given the thirteenth tale.