The novel is set in the country town of Hollingford, England during the 1830's. This is a time when technical and scientific advancements are bringing about great social change. The small provincial town of Hollingford has thus far been little affected, but that is soon to change with the advent of the railway, which will change small town life in Britain forever.
One day, two local women- Miss Phoebe and Miss Browning- take the young Molly with them on a visit to the local estate of Lord and Lady Cumnor. While there, Molly wanders off and falls asleep under a tree, where she is found by Lady Cuxhaven, one of the Cumnor's daughters, and Mrs. Kirkpatrick, the Cumnor's former governess who is visiting. She is generally referred to as Clare, which was her maiden name. Clare puts Molly in her own bed to sleep, promising to wake her in time to go home with her party, but forgets to do so, and Molly is left behind. She is upset at the thought that she will have to remain at the Cumnor's estate overnight, intimidated by the family, and is relieved when her father arrives to take her home.
When Roger arrives, it is with bad news: Osborne failed his exams at Cambridge miserably, and has lost his scholarship. Roger, on the other hand, despite his parents' low expectations, has done very well. The Squire is angry and disappointed in his heir, and the grief and stress adversely affects Mrs, Hamley's precarious health. As she weakens, she leans more and more on Molly, whom she now regards as a daughter.
The next day, Molly and her father reconcile, Molly hiding her hurt feelings and sadness. To her dismay, her father insists on taking her to the Cumnor's estate so that she and Hyacinth (Mrs. Kirkpatrick) can get to know each other better. Molly steels herself for the ordeal, reminding herself of Roger's advice. It takes all her resolve, as Mrs. Kirkpatrick doesn't improve on acquaintance. Though not a bad person, Hyacinth is vain, selfish, and silly, which is obvious to Molly, but her father doesn't seem to notice- probably because he's busy working, and hasn't actually spent much time with his fiancee.
The time for the wedding rolls around, and Molly must leave Henley Hall, as she is to stay with the Miss Brownings during her father's wedding journey. Lord and Lady Cumnor attend the wedding, along with their unmarried daughter, Harriet, who takes quite a liking to Molly's polite yet plain-spoken manner. Molly also meets their estate agent, Mr. Preston, who it seems knew Mrs. Kirkpatrick- now Gibson- some years previously. He also knew her daughter, Cynthia, whom he describes in admiring terms, and he's very interested to hear that she's coming to live with the Gibsons once she finishes school in France.
Molly finds Mrs. Hamley bedridden. She tells Molly that the Squire is extremely angry with Osborne, not so much for doing so poorly, which is certainly disappointing, but because he has also run up astronomical debts. When he failed to obtain his fellowship, the people to whom he owes money applied to the Squire for it- money which he can ill afford. He has been engaged in reclaiming flooded land by having drainage ditches put in an expensive procedure- and the cost of Cambridge for two sons has also stretched the family finances. Squire Hamley is forced to cancel the reclamation project, which also unfortunately puts many local men out of work, adding to his anger and regret. Worse, Osborne refuses to disclose what he spent all the money on, which leads the Squire to imagine all sorts of improper and/ or shameful things. He has ordered Osborne not to come home until he comes up with some money to pay off some bills, and now they're not sure where he is.
Despite Dr. Gibson's best efforts, Mrs. Hamley just gets weaker and weaker. He writes a letter to Roger, and encloses in it another for Osborne, assuming that Roger will know how to get in touch with him, telling them that they'd better come home if they want to see their mother again. Roger comes home immediately from school, and though he doesn't know exactly where Osborne is, he gave the letter to a close friend of his brother's who will know how to get it to him.
Osborne arrives from wherever he was, which relieves his mother's troubled mind, though there is a lot of tension between him and his father. Then, by accident, Molly comes into possession of Osborne's great secret. One day, she enters the library and finds Osborne. She apologizes for interrupting him, but he says she's not, and so she goes to the bookshelves to look for a book to read. While she is there, Roger enters and, not seeing Molly, tells Osborne that he picked up the mail and there's a letter from Osborne's wife. Panicked, Osborne demands that Molly swear to tell no one- which she has no intention of doing- and that she try to forget what she heard. Roger, who is more rational, tells Osborne that of course Molly won't betray him, and also comforts Molly, telling her it was his fault, not hers. Shocked and upset, Molly does her best to put the matter out of her mind, and the three of them don't speak of the matter again.
Soon after this, Mrs. Hamley falls into a coma-like state, unable to recognize anyone any longer, and Dr. Gibson insists that Molly, who is exhausted emotionally and physically, come home. Though immersed in their grief, the Hamley men bid her farewell with gratitude and affection: Osborne giving her flowers, Roger supplying her with books, and the Squire, unable to find words, embraces her as he would a daughter. Knowing that she will never see Mrs. Hamley again, Molly sadly leaves Hamley Hall.