In Chapter XXXVI, it is clear that Lucy and M. Paul have become close friends. Lucy is aware of his Catholicism, however, and she is apprehensive that the difference in their religions will keep them apart. As is his custom, M. Paul leaves improving reading material in Lucy's desk. One day Lucy finds there a pamphlet on Catholicism. Lucy is far too British in her religious feelings; the pomp and circumstance and the "superstitious" beliefs of Catholicism are not for her. M. Paul, Lucy finds out, was made to give this pamphlet to her as part of his penance, given him by Père Silas, for being such close friends with a Protestant.
M. Paul digs in the garden that evening, and Lucy finds him. They discuss the pamphlet, but she does not give any indication that she is sympathetic or susceptible to conversion. M. Paul distractedly tells Lucy that it is dangerous for them, on opposite ends of Christianity, to be friends. Lucy reminds him that they are both Christians, and it is not as if she is trying to subvert his faith in any way. Lucy explains her difficulties with Catholicism, and she tries to convince M. Paul that Protestants are not as bad as Père Silas says that they are. That one of the main tenets of Lucy's Protestant Christianity is that each person's relationship with God is one’s own responsibility is something that neither Père Silas nor M. Paul can understand. M. Paul still hopes that Lucy will convert, and Lucy wonders why she does not hope the same for M. Paul.
Père Silas now comes often to Madame Beck's in an attempt to convert Lucy to Catholicism. While Lucy and M. Paul know that Lucy will not convert, he, however, has come to understand her piety and accept it as a true faith.
In Chapter XXXVII, "Sunshine," the engagement of Polly and Graham is made known. Paulina, always thinking of others, is afraid to tell her father because he doubtless will be sad to lose her.
Dr. John has become a better person for being in love with Paulina since he desires so much to please her—and she only desires good things. Paulina and Lucy discuss him often, and Lucy, though inwardly pained, is truly happy for Paulina and Dr. John, a good match.
M. de Bassompierre has figured out that his little daughter has grown up and that she is probably being pursued by Dr. John. One night after dinner at the Hotel Crécy, M. de Bassompierre and Lucy talk about the couple. They will not marry, of course, without M. de Bassompierre's permission. Though M. de Bassompierre is obviously grieved at losing his daughter, he is reasonable. Lucy appeals to that reason by saying that Paulina is beautiful and rich and will no doubt be very sought-after. It is better to have her marry someone M. de Bassompierre knows, namely Dr. John.
Paulina comes in with a letter written to Dr. John, which her father asks her about. Now directly questioned, Polly can no longer hide her love for Dr. John. She loves her papa more than anyone else, but she also loves her John Graham Bretton. She is worried that this will make her father unhappy, and, unselfishly, she says that she will give Graham up if he wants her to. M. de Bassompierre has no illusions about Dr. John, and he points out some of his faults. The scene is tense, but M. de Bassompierre says that she may marry Dr. John. Polly cannot bear this grudging approval; she declares that she will never leave her papa.
Dr. John comes, and Lucy intercepts him. She explains that Polly is very devoted to her father and cannot bear his anger at their secret attachment. The two men meet and verbally battle over Polly. Paulina makes them shake hands and be friends, and the engagement is settled.
John and Polly marry, and Lucy reflects that there are people whom God has smiled upon. As an outsider, Lucy peers in at their happiness, thinking it perpetual and perfect. They may have some trials in their life, Lucy thinks, but they will lead a much more happy and blessed life than she will. The two do live together happily with many children, blessed by God.
In "Cloud," Chapter XXXVIII, Lucy is surprised to learn that M. Paul is leaving Europe for Guadalupe—lessons will be suspended until a new professor can be found. While outwardly composed, she is very sad and puzzled.
M. Paul and Lucy had discussed Lucy's dream to open a small school one day. Since the pair had come to an understanding about each other's religions, theirs had been a happy and easy friendship. They talk more often than before, and in a weak moment M. Paul had once called her his good friend and sweet consolation. Lucy had wondered if he indeed felt toward her only as a brother might. They had been holding hands at that moment, and perhaps M. Paul would have asked to marry her. But they had been interrupted by Silas and Beck, and the moment had passed.
On the day M. Paul is to leave, Madame Beck tries to keep Lucy upstairs translating a letter for her. Lucy gets away, however, and sees M. Paul leaving. He does not see her. Lucy feels abandoned by him until she receives a note from him. M. Paul will see her before he goes, it assures her, but he is very busy doing something mysterious right now, so she will have to wait.
Lucy waits for M. Paul nervously in the classroom the night before he is supposed to leave. He does not come, and Madame Beck comes and tries to persuade Lucy to go to bed. M. Paul, Lucy says, has always been wanted by Madame for herself, because it would save so much money and be so advantageous for the school. Lucy stormily accuses Madame of being a sensualist, saying that she cares only for herself and for her pleasures. Madame, ever self-possessed, says that M. Paul cannot marry–will not marry. Lucy refuses to go to bed, and Madame leaves her. To the end of their lives they never refer to this "fiery passage" again, and their relationship is untouched by this exchange.
Lucy waits up the entire night. She does not see him the next day, and that night Lucy paces the classroom again. Madame Beck sends Ginevra Fanshawe down to get her, and Lucy, not willing to have yet another inane exchange with her, goes to bed. The maid Goton gives Lucy a sedative that Madame had tried to get Lucy to take the previous night, but it puts Lucy into a curiously energized, possibly hallucinatory state. Lucy gets up and puts on her large sunhat and shawl to disguise herself. She knows of a narrow gap in the fence around the garden, and Lucy herself is so thin that she believes she will be able to slip through it.
In Villette in the Haute-Ville (high town) it is a night of a fête. A carriage which has both the Brettons and the de Bassompierres in it rattles past Lucy, and she follows it. Music is playing in the public space, and though she can no longer see her four friends, she stops to listen to the music. M. Miret, the bookseller who supplies the school, recognizes Lucy. He is generally considered to have a bad temper, but he has always been kind to Lucy. He finds a better seat for Lucy to view the entertainment, and he withdraws. Lucy remembers that he is a friend of M. Paul.
The Brettons and de Bassompierres are sitting nearby, but they do not see her. Mrs. Bretton remarks to M. de Bassompierre that she wishes she had invited Lucy along with him. Lucy, for once, overhears someone saying something nice about her. Dr. John turns and sees Lucy, but she wards him off with a gesture. It is not clear that he actually knows that it is she, in her large hat. They exchange a look that, to Lucy, means that she still has his sincere friendship, even if his affection has now been taken up by Polly.
Lucy wants to be alone, so she leaves. Near the edge of the crowd are the children and families, and Madame Beck is in a company including her eldest daughter Desiree, Père Silas, and Madame Walravens. Lucy calls them the "conjuration, the secret junta" of people who have conspired against Lucy to send M. Paul away. Lucy does not want to risk being discovered, so she remains in the shadows.
A sedative drug, a daring escape, a disguise, and a voyeuristic desire to remain unseen while watching others all combine into another curious episode in this section of the novel. Brontë is fond of putting her characters out on a limb in a physical and atmospherically ominous way, while still keeping them within the bounds of propriety. It was rather shocking for Lucy to escape the school and wander about town at night by herself. That a kindly man, M. Miret, helps her to a seat and seems to recognize her despite her (ridiculously thin) disguise, provides comfort, however, and it is a relief that she is not accosted or bothered by anyone. But Lucy has been up for two days and has a drug in her system and very little food, so she cannot be expected to take necessary precautions.
This is the moment when Lucy can observe the rest of life–people who have things that she wants—Dr. John and Polly have each other; Mrs. Bretton and M. de Bassompierre are independent and wealthy; Madame Beck has friends, family, children, and runs her own school—but who are not in any objective way superior to her. To realize that these people, in direct or indirect ways, can and have taken away any chance at happiness that Lucy might have had, hits home this night, but she accepts it and converts it, in her own way, to her own will. Lucy will have her independence yet.
M. Paul's excruciating refusal to see Lucy adds to the suspense of these chapters. The reader wonders, Why is he going? Will he be gone forever? Have his feelings for Lucy changed? This strong, sometimes vicious, imperious little man cannot be subdued by Lucy, and he cannot subdue (or convert) her. The bonds of affection may still be there, but that does not mean any real practical happiness can result.
Lucy's refusal to convert might inspire as much admiration in M. Paul as her conversion would have gladdened him. He admires her conviction and, during their conversations on religion, M. Paul comes to respect Lucy's heart and faith more because of her clear understanding of how her soul needs to relate to God. M. Paul finds that it is not at all unlike how his soul feels about God, and this deepens their bond. It is, ironically, something of a victory for the unity of the Church.
When Lucy sees Graham at the fête, she now knows that any relationship between them, however much she might have desired it at the time, would have been disastrous. He is too vain, too self-absorbed, and too worldly for Lucy even if he had returned her love. That she would fall in love with a self-important little professor could not have been anticipated, nor could the impossibility of her ever being with him have been foreseen. But she knows that Dr. John does care about her in some small way. His love may have gone to Paulina Mary, but there is still friendship between John and Lucy, and she is thankful for it.