The novel opens with young Molly Gibson, who has been raised by her widowed father, Mr. Gibson. During a visit to the local aristocratic 'great house' of Lord and Lady Cumnor, Molly loses her way in the estate and falls asleep under a tree. Lady Cuxhaven (one of the daughters of the house) and Mrs. Kirkpatrick (an ex-governess to the Cumnor children) find Molly in her slumbering state and Molly is put to bed in Mrs. Kirkpatrick's room. There are allusions to the latter as Miss Clare, her maiden name. Clare appears to be a kind woman and assures Molly that she will wake her up when it is time for the entourage to leave. However, she forgets to do so and Molly is stranded in the mansion. She is distressed at the thought of spending the night at the mansion. To her relief, her father arrives to collect her.
Seven years later, Molly is described as an attractive and rather unworldly young woman, which arouses the interest of one of her father's apprentices, Mr. Coxe. Mr Gibson discovers the young man's secret affection and sends Molly to stay with the Hamleys of Hamley Hall, a gentry family that purportedly dates from the Heptarchy but whose circumstances are now reduced. Molly forms a close attachment with Mrs. Hamley, who embraces her almost as a daughter. Molly also befriends the younger son, Roger. Molly is aware that, as the daughter of a professional man, she would not be considered a suitable match for the sons of Squire Hamley. The elder son Osborne, is expected to make a brilliant marriage after an excellent career at Cambridge: he is handsome, clever and more fashionable than his brother. However, he has performed poorly at university, breaking the hearts of his parents. Molly accidentally discovers his great secret: Osborne has married for love, to a French Roman Catholic ex-nursery maid, Aimee, whom he has established in a secret cottage as he is convinced that his father would never accept Aimée as his daughter-in-law.
During Molly's absence from the house, Mr. Gibson contemplates a second marriage. He expects that marriage will improve his domestic comfort and provide Molly with a mother figure to shield her from influences such as Mr. Coxe. He finds Miss Clare ideally matched to his requirements and recalls her apparent kindness to Molly many years ago. Molly remembers her from their previous encounter and has little love for her. For her father's sake, she does her best to get on with her socially ambitious and selfish stepmother, but the home is not always happy. However, Molly does find an ally in her new stepsister, Cynthia, who is about the same age as Molly. The two girls are a study in contrasts: Cynthia is far more worldly and rebellious than Molly, who is naive and slightly awkward. Cynthia has been educated in France, and it gradually becomes apparent that she and her mother have secrets in their past, involving the land agent from the great house, Mr. Preston, who is rumoured to be a gambler and a scoundrel.
Osborne Hamley's failures make his invalid mother's illness worse and widens the divide between him and his father, which is amplified by the considerable debts Osborne has run up in maintaining his secret wife. Mrs Hamley dies, and the breach between the squire and his eldest son seems irreparable. Younger son Roger continues to work hard at university and ultimately gains the honours and rewards that were expected for his brother. Mrs. Gibson tries unsuccessfully to arrange a marriage between Cynthia and Osborne, as her aspirations include having a daughter married to landed gentry. Molly, however, has always preferred Roger's good sense and honourable character and soon falls in love with him. Unfortunately, Roger falls in love with Cynthia and when Mrs. Gibson overhears that Osborne may be fatally ill, she begins promoting the match. Just before Roger leaves on a two-year scientific expedition to Africa, he asks for Cynthia's hand and she accepts, although she insists that their engagement should remain secret until Roger returns. Molly is heartbroken, and struggles with her sorrow and her knowledge that Cynthia lacks affection for Roger.
Cynthia reveals to Molly that several years before, when she was just fifteen, she promised herself to Mr Preston following a loan of 20 pounds that she needed for a party dress. Mr Preston is still obsessed with Cynthia, but she hates and fears him for the power he holds over her (namely the letters she wrote to him at this period promising to marry him). Molly intervenes on Cynthia's behalf and manages to break off the engagement and get back the letters; however, this creates rumours that she is involved with Preston herself, causing her to be the subject of malicious gossip. This leads to an emotional scene in which both Dr Gibson and Mrs Gibson discover Cynthia's involvement with Mr Preston. After this, Cynthia breaks off her engagement to Roger, sustaining rebukes and insults for her inconstancy, then quickly accepts and marries Mr Henderson, a professional gentleman she met in London. Molly's reputation is only restored after she goes driving with Lady Harriet Cumnor, who is well aware of how fickle public opinion can be and wants to help Molly. Osborne, ill and convinced that he will die soon, begs Molly to remember his wife and child when he is gone. Osborne dies shortly thereafter, and Molly reveals the existence of his wife and child to the grieving Squire Hamley. Osborne's widow, Aimee, arrives at Hamley Hall after receiving word that her husband is ill, bringing with her their little son, named for his uncle Roger but called "little Osborne" in honour of his father. This child, little Osborne, is now the heir to Hamley Hall. Roger has rushed home to be with his father, and his affection and good sense help the squire to see the possible joy to be had in this new family, especially the grandson. He manages to overcome his xenophobia and prejudice against Aimee's Catholicism and asks them both to live with him.
As he resettles into the local scientific community, Roger begins to realise that his affection for Molly is more than that of a brother for a sister. Aided by the kind interference of Lady Harriet, who has always recognised Molly's worth and charms, he finds himself pained at the thought of Molly with anyone else. Still, he hesitates at giving in to his feelings, feeling unworthy of her love after throwing away his affection on the fickle Cynthia. Before he returns to Africa, he confides his feelings to Mr Gibson, who heartily gives his blessing to the union. Roger is thwarted, this time by a scarlet fever scare, in his attempt to speak to Molly before he leaves. At this point, Gaskell's novel stops, unfinished at her death. She related to a friend that she had intended Roger to return and present Molly with a dried flower (a gift Molly gave him before his departure), as proof of his enduring love. This scene was never realised and the novel remains unfinished. In the BBC adaptation, an alternative ending was written in which Roger is unable to leave Molly without speaking of his love, and they marry and return to Africa together.