The story centers on a wild, high-spirited Kentucky girl known as Miss Lady, who grows up in a neglected old mansion called Thornwood under the affectionate care of her father, Colonel Bob Carsey. Her carefree existence is challenged when she meets Donald Morley, a restless and impulsive young man from the city. Despite her father's disapproval, a deep romance blossoms between them, filled with outdoor rides and shared adventures. Their happiness is abruptly tested when Donald becomes entangled in a violent shooting incident involving a local ex-pugilist and a wealthy suitor, leading to his hasty departure.
Following a fatal accident on the railway that claims her father's life, Miss Lady is left alone and bewildered. Amidst her grief, she struggles with conflicting loyalties, holding to a promise made to her father while silently longing for Donald, who has vanished abroad without explanation. During this lonely period, she finds solace in the intellectual companionship of Doctor John Jay Queerington, an old friend of her father's who eventually becomes her husband. Yet, this marriage, built on respect and reliance rather than passion, leaves her wrestling with an unfulfilled emotional void.
Years later, Donald returns home to face the legal charges against him and clear his name. His reappearance forces Miss Lady to confront the profound regrets of the past and the reality of her present life. Against a backdrop of social pressures, family secrets, and the rustic charm of rural Kentucky, the narrative builds toward a resolution where long-buried truths emerge, altering the lives of everyone on Billy-goat Hill.