Emily arrives in Thoulouse, where she is surrounded by memories of happy times with Valancourt, and this makes her melancholy. She even starts to imagine that she sees Valancourt lurking around the estate. One morning, Annette casually mentions that the gardener caught sight of an intruder and shot him. The intruder was wounded, but managed to get away. Emily is fearful that this stranger may have been Valancourt. Saddened by the idea that he might be hurt, Emily moves on to La Vallee, where she is comforted by memories of her father. Monsieur Barreaux visits her, and Emily also tracks down Theresa. Emily notes that Theresa is living in a comfortable cottage, and Theresa explains that she has a secret benefactor, but cannot reveal who it is. Theresa also speaks nostalgically about Valancourt and how wonderful he was. Emily becomes frustrated and tells Theresa to stop speaking about Valancourt, but Theresa objects that Valancourt has been taking care of her ever since Monsieur Quesnel dismissed her from her job. She also explains that Valancourt hasn't made his usual visit, and she is growing alarmed, which confirms Emily's suspicions that Valancourt might have been injured in Thoulouse. Emily discreetly sends a servant to the home of Valancourt's brother to see if she can find out any information.
Meanwhile, the Count de Villefort and Blanche have had a nice visit at the St. Foix estate. Blanche and the Chevalier St. Foix are now engaged and plan to wed soon. Blanche, the Count, and the Chevalier set off together to visit Emily at La Vallee, which involves a perilous journey through the Pyrenees mountains. They lose their way, and as night falls, they decide to ask for shelter at a remote fort. They are a bit nervous, because the Count explains that these forts are often occupied by Spanish smugglers and robbers, but they don't want to spend the night out in the open. The men staying at the fortress seem to be hunters, and they agree to let the travelers spend the night there. However, when Blanche gets lost trying to find her bedroom, she overhears the hunters talking about their plans to murder the travelers. They seem to be smugglers and thieves, not hunters. Blanche wants to warn the others, but becomes overwhelmed, and faints. When Blanche awakens, the Chevalier St. Foix and the Count are both wounded, but they have fought off the smugglers and trapped them in the dungeon. Ludovico is also there. Since more smugglers are expected to return to the fort, the group quickly hurries away, even though the wounds of the Chevalier are somewhat serious.
Back in Gascony, Emily goes to Theresa's cottage to ask about Valancourt, but no one has heard anything, and Emily is increasingly convinced that Valancourt must be dead. Suddenly, Valancourt himself shows up at the cottage. He was indeed wounded by the gardener at Thoulouse, and had to spend time being treated, but is now mostly recovered. He notices that Emily still seems to care for him, and gives a ring to Theresa, asking her to pass it along to Emily. Back at La Vallee, Emily and Annette are shocked when Ludovico turns up. He explains that after escaping from the fort, the Count, Blanche, and the Chevalier had to stop in a village so that the Chevalier could receive medical attention. The Chevalier will soon be joined by his father, and Blanche and the Count will be arriving at Le Vallee soon. In the meantime, Ludovico finally explains where he has been all this time. While Ludovico was spending the night in the rooms of the Marchioness, several men entered via a hidden door in the wall. They tied him up and sneaked him out of the castle through a series of secret passages, and then transported him to the fort in the Pyrenees. The smugglers are also pirates, who hide their stolen treasures in the unused rooms of the chateau. The strange sounds and movements have led to the rumors of the rooms being haunted, and the pirates have benefited from the rumors because it prevents them from being discovered, and discourages anyone from investigating the rooms too closely. Ludovico languished in the fort until he overheard talk of plans to harm the Villefort travel party, and sprang into action to help them. This defeat also allowed him to finally escape.
After a short visit at La Vallee, the Count de Villefort, Emily, and Blanche all travel together back to Chateau Le Blanc, where they meet up with Du Pont and the rest of the Villefort family. The Count tries one more time to persuade Emily to marry Du Pont, but she refuses. Instead, Emily hurries to the monastery of St. Claire, where she learns that Sister Agnes is dying. A man named Monsieur Bonnac has come from Paris to see her, but a nun also mentions that Agnes has been asking about Emily, and suggests Emily visit her. Emily reluctantly agrees, and goes to Agnes' room. When she sees Emily, Agnes becomes distressed and starts raving about a crime, and someone coming to punish her. She also asks Emily if she is the daughter of the Marchioness de Villeroi. Emily is confused, and Agnes shows her a picture of the Marchioness; it is indeed identical to the picture St. Aubert had in his possession. Agnes also shows Emily a portrait that Emily recognizes from the portrait she saw at Udolpho: it is Signora Laurentini. Although she has changed considerably, Sister Agnes explains that she is the woman in the portrait. Emily starts to put together Agnes' mysterious guilt, the timeline of when she disappeared and entered the convent, and also the hideous sight she had uncovered under the veil at Udolpho. She starts to think Agnes might be a murderer, and flees in horror.
Back at the Chateau Le Blanc, Bonnac comes to join the group because he is a friend of the Count's. Bonnac comes from a noble French family, and his wife is distantly related to Sister Agnes, hence why he was summoned to her bedside. Bonnac's family has had a lot of financial troubles, and he was even put in prison due to the debts. However, a good friend paid off Bonnac's debts, and helped him and his family—and it turns out this man was Valancourt. Bonnac explains more about what Valancourt's life in Paris was like: he did indeed start gambling, and spent some brief time in prison for debt, but he used this time to realize that he wanted to turn his life around. As soon as he got out, he used all the money he had left to help Bonnac, and Valancourt never had any mistresses, despite false rumors. When Du Pont and the Count hear all of this, they realize that Valancourt is a good man, and Du Pont accepts that he will never be with Emily. The Count also invites Valancourt to come and visit them at Chateau Le Blanc.
Word comes from the convent that Agnes has died; she leaves a significant portion of her wealth to any descendants of the Marchioness de Villeroi. A nun who had heard the full history on Agnes's deathbed meets with Emily, and finally explains the whole story. Signora Laurentini was born a wealthy Italian noblewoman in the region near Venice; her parents died when she was young, and she inherited the castle of Udolpho, as well as other lands and estates. However, the Signora was spoiled and stubborn. She met the Marquis de Villeroi when he was traveling in Venice, and the two of them fell in love. However, the Marquis made her false promises of eventual marriage in order to have an affair with her, and then left for France. Agnes/the Signora waited for him at Udolpho, where she rejected Montoni's courtship (leading to the story that she turned down Montoni because she was in love with another man). Eventually, Agnes/the Signora learned that the Marquis had gone ahead and married a French woman; frantic, she secretly left Udolpho and hurried to France. This explains the strange disappearance of the Signora, and how Montoni came to inherit the castle.
In France, Agnes found a place to stay not far from the Chateau Le Blanc, and confronted her lover. She and the Marquis began having an affair again, and she gradually started to turn him against his wife. The Marchioness didn't marry the Marquis willingly, and had been in love with another man. Agnes lied and told the Marquis that his wife must still be having an affair with her beloved; he believed Agnes, and became so obsessively jealous that he poisoned the Marchioness. After the crime, both Agnes and the Marquis were consumed by guilt. The Marquis closed up the chateau, and went abroad, while Agnes fled to the convent, and gave a false story of why she was hiding in the convent (the story Sister Frances told Emily, about Agnes having been an adulterous wife). Moreover, the Marchioness of the Villeroi was the sister of St. Aubert, and therefore Emily's maternal aunt. Monsieur St. Aubert knew that his sister had suffered and likely died an untimely death; he kept papers related to this, as well has her portrait, hidden in La Vallee. Upon her death, Agnes left some money and property to Bonnac's wife, and some to the descendant of the Marchioness, who turns out to now be Emily. It also turns out that the hideous sight hidden behind the black veil is not what it seems: Emily had thought it was the decaying face of a dead body, but it is a wax figure that a former owner of Udolpho was required to keep on display as punishment for a crime.
Valancourt arrives at the Chateau, and tells Emily about his past. She realizes she has been mistaken, and the two vow their love to one another. A short time later, Emily, Blanche, the Chevalier St. Foix, and Valancourt have a double wedding. Annette and Ludovico also get married, and Emily gives them money and some land from her estate. Emily sells the estate at Thoulouse, and uses the profit to buy the rest of her ancestral estate back from Monsieur Quesnel. Since Valancourt's brother also gives him some land, Emily and Valancourt end up with lots of land in France, although they still spend most of their time at La Vallee. Emily also gives all the Italian property she inherited from the Signora Laurentini to Bonnac, who is now also the owner of the castle of Udolpho.
The final section of the novel focuses on achieving resolution for the various "mysteries": when Radcliffe chose the title of her novel, she lured her readers with both the promise of suspense, but also the satisfaction of resolution. In keeping with the theme of seemingly supernatural events being given pragmatic conclusions, the mystery of what was happening in the rooms of the Marchioness ends up getting an entirely practical explanation. In fact, the seemingly ghostly events can be explained by human greed and economics: the smugglers want to gain wealth, and they exploit fear in order to do so. This revelation is in keeping with many of the other plot points in the novel: while Emily is often afraid of ghosts, specters, and strange noises in the night, the real threats are driven by greed and a desire to secure money and power. Radcliffe hints that humans should actually be afraid of each other and the economic systems they create, rather than looking for more supernatural threats. The resolution of the smuggler plot also allows Ludovico to distinguish himself as a heroic figure in spite of his lower class position, suggesting that many different types of character can engage in heroic and noble actions. By protecting the group of travelers and helping to save their lives, Ludovico earns the money and property that he and Annette will receive at the end of the novel. The incident with the smugglers also allows for a parallel reconstruction of events at Udolpho: this time, it is Lady Blanche who is in danger due to being trapped in a mysterious building with sinister foreign men, but she is also rescued just in time.
With the death of Agnes, Emily also pieces together some important information that connect events at Udolpho with events at Chateau Le Blanc, and sheds light on her own family history. Emily has always felt an inexplicable pull towards the Marchioness, and now learns that this woman was actually her paternal aunt. The Marchioness shared many traits with Emily, and her tragic fate represents what might have befallen Emily if she had ended up trapped in a marriage with a cruel or jealous man. The Marchioness' fate showcases the vulnerability of women under systems of patriarchal control: first her father and then her husband exerted absolute control over her body and her life. Her father, St. Aubert, mourned for her, but furthered a type of silencing by hiding her story from everyone, including Emily. It is only through the unfolding of all these strange and convoluted events that Emily is able to resurrect the connection between herself and her aunt. By hiding her story and the events of her life, St. Aubert also participated in the oppression of his sister, even though he loved her. While the explanation of the "haunting" partially relies on the revelation about the smugglers, there is also the sense that the ghost of the Marchioness has been laid to rest because someone finally knows her story, and can carry her memory forward.
The information that the Marchioness was a victim of masculine domination and abuse is not surprising, given what has already happened in the novel. What is shocking is the revelation of how strongly another woman contributed to her fate. The false backstory of Sister Agnes already hinted that she had been less passive, and more ethically compromised than other women in the novel, but the true story shows her as even more willful and driven by her passion. The portrayal of Agnes/Signora Laurentini's biography provides some contextual clues for her subsequent shocking behavior: like many other Italian characters, she is portrayed as innately more volatile, violent, and emotional. As an orphan, she also lacked the wisdom and guidance of parental figures, and in contrast to someone like Emily, Agnes/the Signora is portrayed as someone who never learned to restrain her emotions or desires. All of these factors culminated in her obsessive desire for the Marquis, and her pursuit of him. If the Marchioness represents the dark fate of a dutiful and submissive woman, Agnes/the Signora represents what happens when a woman gives in to unbridled desire. Throughout the novel, Emily has had to carefully navigate between these poles. She has refused men she didn't care for, but she has also never given into her passion and done something like elope with Valancourt.
Sister Agnes has been tormented by a guilty conscience throughout her life, showing that true haunting is internal and psychological, not the mysterious sights and sounds of whatever was in the rooms of the Marchioness. She attempts to redeem herself on her deathbed, thus uniting many different plot threads, and finally granting Emily part of the stability she has been seeking through the novel. Emily has been repeatedly failed by the more traditional masculine forces that were intended to protect her: her guardians disappointed her, Valancourt never came to rescue her, and her father failed to ensure she had financial stability. Instead, Emily ends up with a significant amount of money (and the agency that comes from money) being transmitted via female inheritances. In addition to what she does eventually inherit from her father (La Vallee), she inherits from Madame Montoni (Thoulouse), and the Signora Laurentini (money and property in Italy). The money from these unhappy women finally merges and empowers Emily. Because of all of these income sources pooling together, Emily ends the novel fabulously wealthy and able to live life on her own terms. She can secure the entirety of the St. Aubert estate back from Monsieur Quesnel, and honor her father's memory by protecting and preserving it.
More significantly, Emily's new wealth empowers her to marry the man of her own choosing. She now has both the money and the life experience to believe that if she wants to marry Valancourt, she doesn't require anyone else's permission in order to do so. Of course, what also leads Emily to want this marriage is the resolution of another "mystery": what Valancourt was up to in Paris. The last minute introduction of yet another character (Bonnac) allows for further information and clarification, and the news that Valancourt is actually much more honorable than he seemed. This misunderstanding is yet another example of Emily's imagination rushing to more dramatic and less plausible conclusions, rather than carefully investigating the reality of what was actually happening. While Valancourt's honor is restored with this information, he never fully returns to the role of masculine hero and remains interestingly passive. It is Emily's fortune that largely secures their future together, and he notably goes to live with her on her estate. While Emily's lack of protection has made her vulnerable throughout the novel, it also ultimately gives her the agency to choose and build a life for herself. Her return to La Vallee marks Emily coming full circle, and finally returning to the one place that has been a space of safety and sanctity. However, rather than retreating back to childhood, Emily returns as someone who has finally attained adult maturity, and can now form her own family. The resolution of the marriage plot is important, but as Scott MacKenzie explains, the marriage is deeply embedded with Emily securing a sense of home: "Tying marital knots is a compulsory ritual in Radcliffe resolutions, but the establishment of a happy home receives investment that consumes marriage. Home is, above all, the narrative's destination" (416).