Lucy watches Père Silas, Madame Beck, and Madame Walravens for a while. The school gossip was that these three had hatched the plan to get M. Paul to leave for Guadalupe. Madame Walravens has had a dowry estate in the West Indies that was not profitable during her financial troubles. It has been cleared of debt and is now available to be made profitable by someone who can run an estate well. Madame Beck knows this and is angling to become Madame Walravens's heir. Père Silas would like to have a foothold in the Caribbean, for he has a missionary zeal. They need M. Paul to go to Guadalupe and run the estate to make it profitable. After M. Paul has done so, he may return to Villette and live his own life. Though the distance to Guadalupe is far and the climate is hazardous, Lucy learns that these three are willing to let M. Paul risk his life for their own interests.
They are talking about "Justine Marie" coming, and Lucy, fearing that she is hallucinating, wonders why they are expecting a dead person. This Justine Marie turns out to be M. Paul's ward and a relative of the Walravens and Madame Beck, named for her dead aunt (the Justine Marie who had been affianced to M. Paul). She arrives with M. Paul and her aunt and uncle. Lucy, spying through the trees as Madame Beck might have, learns all this and now knows that Justine Marie is not the woman in the portrait or the spectral nun in the garden or grenier–for that nun is much, much taller than short Justine Marie. But Lucy, now seeing M. Paul gay with this party of his friends and relatives, believes that when he returns from the Caribbean he will marry this wealthy heiress. It turns out that M. Paul has changed his travel plans and is leaving on a different ship in a few days.
Lucy must return to the dormitory before she is caught. As she walks home in the dark, a carriage goes swiftly by her and a white handkerchief is waved out the window. She does not know who has waved at her, and she hopes that she has not been discovered. When she reaches her own bed she finds the ghostly nun's clothing with a note that says "The nun of the attic bequeaths to Lucy Snowe her wardrobe. She will be seen in the Rue Fossette no more." Lucy notices that the clothing is too long for the height of any woman that she knows, so it must have been worn by a man. But she does not know of any man who would do such a fearful thing as a false haunting. Relieved, however, that the nun was never a ghost or spirit, she bundles up the clothes under her pillow and goes to sleep.
In Chapter XL, "The Happy Pair," Ginevra Fanshawe has disappeared. Mrs. Cholmondeley is blamed for it, but Lucy remembers the waving handkerchief and guesses the truth: Ginevra has eloped with the Count De Hamal. Lucy learns from Ginevra's uncle M. de Bassompierre that the Count has large gambling debts, and actually the Count is liable to prosecution for the abduction of a minor. Since Ginevra is underage, too, the two are not even legally married. It is a scandalous affair, but Lucy is not surprised; Ginevra is a flibbertigibbet.
Lucy receives a letter from Ginevra explaining how De Hamal assumed the disguise of the ghostly nun in order to visit Ginevra. They would meet in the attic where Lucy first saw him, getting in by means of the skylight.
Ginevra is now a Countess like her cousin Polly. It appears that a large part of Ginevra's motivation in elopement was to spite both Dr. John and Paulina, for in Ginevra's twisted mind they have wronged her by being in love with each other. That neither Dr. John nor Polly cares what Ginevra has done does not seem to enter her mind.
Ginevra eventually apologizes to Lucy about the ghostly visitation, and she remains a correspondent with Lucy over the years. She and the Count live in Europe beset by debt and scandal.
As Chapter XLI, "Faubourg Clotilde," opens, Lucy is worried that M. Paul still will not come to say goodbye. Finally he comes to see her. He is sad to see that she looks ill and has been very unhappy.
Another histrionic scene occurs when Madame Beck interrupts and tries to draw M. Paul away. Lucy cries out, "My heart will break," and M. Paul sternly tells Madame to leave. Madame tells him that he must remember his duties, which he says he knows. Madame is intractable, and M. Paul has to shout at her and slap her (it is more a token than an actual blow) before she will leave.
Lucy tells him that she was worried that he would have left without saying goodbye. He says that he will prove to her that he has not forgotten her and that he is her true friend. They go walking, and he tells Lucy that he thought of her constantly while they were apart. Lucy, though now feeling happy, is very pale, and he is worried for her. She worriedly asks him if her face displeases him so much. He tells her firmly (and by this we may infer that a kiss was given) that he likes her appearance. Lucy, for the first time in her life, does not care what the rest of the world thinks about how she looks, so long as she pleases M. Paul.
At Rue Fossette it is very likely that M. Paul's letters to Lucy from Guadalupe will be intercepted or destroyed by Madame and her spies. M. Paul does not want to think of her there missing him and not getting his letters. M. Paul has brought them on their walk to a new part of town called the Faubourg Clotilde. They go to a pretty new building, and after a few minutes it becomes clear that this building has been taken by M. Paul for Lucy to use as a school. All this time M. Paul has been working to create a new school for Lucy to run herself. He was afraid his face would give away the surprise if he saw her before he gave her the keys and the prospectus with her name announcing the new school. Her job now is to maintain her health and to run the school well while he is away, for he plans to come back in a few years.
Lucy and M. Paul dine on the balcony, and he tells her about the house. M. Miret, who found Lucy a seat at the fête, is her landlord, and his daughters will be her first students. When M. Paul tells her that his ward Justine Marie should enroll, too, Lucy reveals that she saw and heard him and Justine Marie and the rest of the family at the fête. She is jealous, believing that he wants to marry her. The two share a tender scene in which he tells her how he loves her—and that when he returns, they will be married. Justine Marie is already engaged to a German, and M. Paul had only ever thought of her as his ward.
Back outside Rue Fossette, Lucy reflects that she once thought him harsh and strange, but that love has changed her opinion of him and indeed of herself. M. Paul pledges to marry her when he returns, and they part. He sails the next day.
The short final chapter, "Finis," tells of Lucy's success at the school. She was happiest while M. Paul was away (she tells us why at the end) when she was building up the school and enjoying her independence and her own work. She makes a library in the Faubourg Clotilde house for M. Paul, and she puts in the plants he likes. Her school does well, and when she receives an unexpected bequest of one hundred pounds from Mr. Marchmont (the cousin of her former employer Miss Marchmont), she uses it to procure the building next door and make the day school into a boarding school.
Lucy has learned that a large part of happiness is working for something not only for herself but for others. She gets long letters from M. Paul, and he says that she should remain a Protestant and that he respects and loves that characteristic of hers.
At the end of three years, M. Paul's ship is due. Lucy sees horrible storm clouds coming, and she prays that his ship is watched over by God. Lucy never tells us what happens to the ship, but it is clear that M. Paul does not make it home alive. It is the fault, of course, of the selfish and grasping Madame Beck, Madame Malravens, and Père Silas, who all end up having lived long and prosperous lives.
While it is strongly implied that M. Paul dies in a shipwreck, the fact that Lucy will not write the words of the event shows the abortiveness that has reigned over much of Lucy's life. She learns to love but never has the consummation of it (like Miss Marchmont, another admired woman in this novel). There has been a suggestion of ghostly visitation and knowledge of a world beyond this realm, but the supernatural turns out to have been a rather sordid disguise used by a young man for illicit visits. While Lucy does have some success in her life (the independence of running her own school was certainly unusual for women of her time—and admirable, even though it was still a job) and has gained some friends, she has lived much of her life looking from the outside in.
M. Paul, surprisingly, brought her into his own heart and his life, and if he had lived, it seems, Lucy and M. Paul would have been happier than the other couples, the self-deluding Ginevra and the selfish Count De Hamal, and the vain and somewhat shallow Dr. John and the dependent, selfless Polly. Lucy’s and M. Paul’s relationship is the only close relationship in the novel that appears to be on adult footing. An interesting pair of bookend scenes have occurred when M. Paul made an extended study of Lucy's face on their very first meeting, in the parlor of Madame Beck's, when he made his physiognomic evaluation of her face, and now on their very last meeting. M. Paul, it is implied, is the only one who ever truly sees Lucy and understands who she really is.
In typical Brontëan fashion Lucy cannot have her strong-willed, dominating, imperious man in the end (for that would impinge upon her independence). That she won his heart and tasted of true love before he was lost will have to be enough for her. Besides the poetic bittersweetness of the ending of this story, it is an example of how Brontë herself viewed the problems of marriage. Deeply conservative in many ways, Brontë had a hard time believing that a good marriage could really include both an independent, free-thinking woman and a self-possessed, confident, masculine man. Thus, in this situation the love is real and is won, but the promise is never fulfilled.
Lucy, who is never fully straightforward with the reader, uses the excuse that she does not want to aggrieve the reader when she reaches the point of telling of the fate of M. Paul's ship. The reader is left to read between the lines, wondering what Lucy really means when she says, "M. Paul is more my own" now that he is dead. Does this possibly mean that she would not, in the end, have been able to marry him? To model Miss Marchmont's life of mourning a dead almost-husband, a live of love-lost independence, must Lucy mean that M. Paul died? Or, despite the implicit statement of his death during the storm, did he simply fail to return from Guadalupe? There seem to be no signs of this alternative, but the reader, as at so many times in this novel, remains uninformed and unsure.
The plotting of Madame Beck and the final rebuttal from M. Paul have been building from the first moment Lucy stepped into her house. Madame Beck, though in her feminine indirectness rather than in her cousin M. Paul's masculine directness, has to control everyone around her, and that includes the enigmatic English teacher in her employ. Madame, though she must know her cousin well enough to know that he would not shirk his duties once he said he would do them, even wants to steal from Lucy the last goodbyes they have together. That M. Paul stands up to her and so obviously chooses Lucy, while still honoring his promise, is a great moment for the almost perpetually forgotten and friendless Lucy.
The ending cannot be that tragic, for Lucy has achieved, through M. Paul, two of the main goals of her life: independence and love. That she cannot partake of the love in the normal fashion of married life (as Polly and Ginevra do) ennobles her, and her early training in adversity perhaps has made it easier for her to bear than it would have been for either of the other girls if they were faced with the same tragedy. Lucy is a triumph of independence who never must lose herself to a man, and she also, at least, has the memory of love and regard to comfort her in her old age.