The novel opens in France, in the year 1584. Emily St. Aubert is a young woman living happily with her parents, Monsieur and Madame St. Aubert on a secluded country estate called La Vallee. Monsieur St. Aubert grew up in a wealthy family, and was once active in the political and social circles of the nobility, but decided he wanted a life of peace and tranquility. Due to money problems, he has sold most of his estate to his brother-in-law, Monsieur Quesnel (the brother of Madame St. Aubert), but lives contentedly with his wife and daughter on a modest portion of it. He spends much of his time reading, reflecting, and appreciating the beauty of nature; he has also passed these traits on to his daughter, and ensured she received a good education. Emily also loves to read, admire the beauties of nature, and compose poetry.
When Monsieur St. Aubert catches a fever, the whole family is very anxious, but he seems to recover. When he grows stronger, the family goes on an outing to their fishing house, where Emily brings her lute. When she forgets it and has to return to retrieve it, she is surprised to hear music being played inside. She waits until the music stops, and goes inside to find that someone has clearly played the lute and returned it to different spot from where she left it. This incident is unsettling because a short time before, Emily had found a copy of a poem left in the fishing house, which seems to have been describing her. Later that day, Madame St. Aubert realizes that she has forgotten a bracelet containing a portrait of Emily in the fishing house, and that someone seems to have stolen it.
Back at their home, the St. Aubert family is surprised by a visit from Monsieur and Madame Quesnel. The Quesnels are obsessed with the superficial glamor and scheming life at the Parisian court, and say insulting things about life in the country. Monsieur Quesnel also offends Monsieur St. Aubert with his plans to modernize and expand the chateau he owns. However, these incidents are quickly forgotten because, after the Quesnels depart, Madame St. Aubert becomes ill with a fever and dies. Her husband and daughter mourn for her, although Monsieur St. Aubert cautions Emily to never abandon herself entirely to her emotions.
In the aftermath of the death, friends and family come to visit the grieving pair. These include a neighbor named Monsieur Barreaux, and Monsieur St. Aubert's sister, Madame Cheron. Madame Cheron is a widow who lives on her own estate near Toulouse, and she invites her brother and niece to come and visit her soon. Emily and her father attend a dinner party hosted by Madame and Monsieur Quesnel on their estate, where the other guests include Madame Cheron and two Italian men, Signor Montoni and Signor Cavigni. In the period after his wife's death, Monsieur St. Aubert's health deteriorates, so he and Emily decide to take a trip in hopes it will improve his health. They plan to travel along the Mediterranean coast towards Provence, and quickly pack up to begin their journey. Before they leave, Emily happens to see her father weeping over a portrait of an unknown woman who is not her mother.
The journey gets off to a good start, with both Emily and her father being deeply moved by the beautiful scenery they witness. Along the road, they encounter a young man named Valancourt, who appears to be hunting and wandering among the wild landscapes, but who is also clearly from a good family. He helpfully guides Emily and her father to a small village where they spend the night, although the rustic conditions are somewhat alarming to them. Valancourt ends up joining them on the next leg of their journey, and his humility, intelligence, and sensitivity impress Monsieur St. Aubert. They eventually part ways.
Shortly thereafter, Monsieur St. Aubert is startled by a voice calling for them to stop. Thinking they are being attacked or robbed, he shoots his pistol—only to realize that is it Valancourt, who has decided to rejoin them. Valancourt has been shot in the arm, so they take him to the town of Beaujeau to receive medical attention. Since they have to spend a few days there while Valancourt recovers, the group gets to know each other even better, and Monsieur St. Aubert likes the young man more and more. They eventually travel onwards together, spending a night at a convent in the mountains, and eventually reach the town of Arles, in the region of Rousillon. From here, the group will part ways, so that Emily and her father can continue their journey along the coast. Everyone is very sad when they separate.
Left alone with her father, Emily finds a book of poetry that Valancourt has left behind, and realizes that he was in love with her. However, her father's health seems to be declining, and Monsieur St. Aubert has also received letters telling him that he has been betrayed by his banker and manager, and has lost a great deal of money. Emily says that as long as they can keep their home at La Vallee, she will be happy. As they travel, St. Aubert gets sicker and sicker, and one night, they find themselves lost in the woods with nowhere to stay and St. Aubert in desperate need of rest. A peasant named La Voisin takes them in, and tells them about the nearby chateau, once owned by the Marquis and Marchioness de Villeroi. Now that they are both dead, it is abandoned; Monsieur St. Aubert says that he knew the Marchioness, and seems haunted by this memory. Before they go to bed that night, Monsieur St. Aubert announces his intention to start the journey home the next day. However, in the morning he is still very ill, and Emily finally realizes that her father is going to die. Monsieur St. Aubert instructs Emily to retrieve some papers hidden beneath the floor at La Valee, and burn them without reading them. He also tells her to never sell their chateau. St. Aubert passes away peacefully.
Radcliffe's novel incorporates many different settings, and often involves characters journeying from place to place. For Emily, much of the novel will be about be her effort to return to her home, and the security and stability she experienced there. Therefore, the beginning of the novel plays an important role in setting the stage for why Emily has such a strong connection to La Vallee, and why it becomes part of her idealized sense of home. La Vallee is presented as an almost Edenic setting, where everything is peaceful and calm, and there are no threats or dangers (which will be an important contrast to many other settings). St. Aubert deliberately chose to retreat away from a more chaotic and sordid world, and built a place of sheltered retreat for himself and his family. Emily's upbringing in this sheltered locale sheds light on her character, revealing why she is somewhat naïve and trusting, and also delicate in her sensibilities. Emily has been highly cultivated and refined, but she is also quite fragile and not necessarily resilient. Much of her character arc over the course of the novel will require her to achieve a new level of maturity and resilience by learning how to actually cope with obstacles, once she is no longer kept safe and coddled by her family.
While the opening of the novel sets the scene for an idyllic and protected life that the St. Aubert family has been leading, it also introduces a number of threats and challenges that will become the backbone of the subsequent plot. The incident at the fishing house seems incidental, and can be easily forgotten as the plot moves forward, but it has both thematic and narrative significance. The sheltered nature of Emily's life implies she has likely not been courted or spent much time around men; although she is at an age where she is available as a marriage prospect, this aspect of her future never seems to have crossed Emily's mind, and she remains quite childlike in this aspect. The idea that someone, presumably a man, has been watching Emily and feeling desire for her marks the end of this childish innocence; for the rest of the novel, Emily will not be able to escape from the reality that men want her, either for her wealth, her beauty, or both. This desirability will often imperil or frighten her, as this first incident reveals: Emily feels unsettled by the mysterious events at the fishing house. The theft of Emily's portrait also introduces some key themes into the text. Portraits of women, including of the Marchioness Villeroi, will become an important plot and thematic element, signaling both women's objectification into passive objects that can be circulated and passed around, but also the hidden histories that might lurk within their subjective worlds. Emily's portrait passes from her mother's possession (implying her status as a child who is cared for and nurtured) into the possession of an unknown man (implying her new status as a sexualized object, who can also be seized and taken against her will).
While St. Aubert has tried to remove himself and his family from as many worldly concerns as possible in order to focus on feelings, beauty, and creativity, he is unable to completely sever ties with the materialistic and economic concerns that are often central to the novel's plot. Radcliffe ostensibly sets the novel about 200 years prior to the time when she was writing, but she only very loosely incorporates this historical setting. The situation of St. Aubert, who comes from a good family but has gradually lost his ability to fund and maintain his family estate (Epourville is the larger estate, now owned by Monsieur Quesnel, whereas La Vallee is a smaller portion) is much more reflective of a problem faced by aristocrats in the late 18th and 19th century. Monsieur St. Aubert does not seem to be interested in money, but he is clearly hurt by the crass way in which Quesnel manages the estate. More significantly, the possible loss of the St. Aubert family fortunes is likely to impact Emily; it means she may not be able to marry if she is no longer an economically desirable prospect. This financial threat shows the dark side of St. Aubert's choice to retreat from the world and forego some of his key responsibilities: he may have inadvertently imperiled his daughter's future.
St. Aubert's situation is all the more difficult because Emily's relations are clearly positioned as a negative force from the very beginning. At the very least, Monsieur and Madame Quesnel are selfish and shallow; their focus on money, status, and fashionable life is in direct contrast with the life Emily has grown up with. These materialistic interests foreshadow other characters, such as Montoni, who will be willing to potentially kill over money and power. At first, it seems like Cavigni and Montoni are only very minor characters, as it is not yet clear that they will be reintroduced, and what role Montoni will play in the plot. The context of the introduction, however, is important: the two Italians are presented as the guests of the shallow and worldly Quesnels, hinting that they are unlikely to be kind and virtuous. Madame Cheron, Emily's other close relative, also seems to hold very different interests and values from her brother, and this exposition around Emily's extended family sets the stage for her to be in a difficult and even dangerous situation after she is orphaned. The relationships between these characters also introduces the persistent theme of tension between country and city life: throughout the novel, cities (particularly Paris and Venice) are associated with vice, selfishness, and immorality, whereas country estates such as La Vallee are places of virtue and happiness. The Quesnels find life in the country to be dull, and prefer to spend all of their time in Paris, which is yet another hint that they are selfish people.
While St. Aubert disapproves of city life, he is open to travel as a way of coping with grief. Once Madame St. Aubert has died, La Vallee will never be the same, and St. Aubert shows a shrewd sense of psychology in wanting to ensure that Emily is exposed to stimulation and change, and does not become lost in her grief. The prospect of their journey will take them south across the Pyrenees mountains to arrive at the coast of the Mediterranean Sea, and from there they plan to move westward (it is important to note that Radcliffe used geography vaguely and loosely, and also sometimes chose names for places that are different from contemporary names for cities and regions). The journey introduces a major aspect of the novel: sections that are essentially landscape description and travelogue. At the time when Radcliffe was writing, it was not easy for individuals to travel to different regions (and the French Revolution and subsequent warfare made France a particularly perilous destination for British travelers). The absence of photography also meant that readers were often interested in reading lengthy descriptions of sights and scenery, which might appear as somewhat tedious to modern tastes. These lengthy and vivid descriptions create the opportunity for Emily and her father to highlight their sensitivity and taste as individuals who can be deeply moved by beauty, and the wonders of the natural world.
The journey marks Emily literally leaving behind the safe and sheltered world of La Vallee, and symbolically, her childhood. Valancourt bears all the marks of a romantic hero and ideal match for her, although Emily interestingly seems to be too innocent to even think of a romantic attachment at first. In fact, it is St. Aubert and Valancourt who seem to spend most of the journey bonding with one another. This close relationship between the two men is important because it implies St. Aubert would have approved of the subsequent relationship that evolves between Emily and Valancourt. It also reflects Valancourt being positioned as the man who should take over responsibility for Emily; had she been married or even formally betrothed to Valancourt when St. Aubert died, Emily would have possessed the security of a male protector. Her vulnerability is created because she is left orphaned, without a father figure to guide her, but has not yet secured a male partner who can protect her and her interests. St. Aubert's death at the end of this section is emotionally devastating for Emily, but it also puts her in a perilous position where she can be manipulated and abused by individuals who have their own agendas. Moreover, the lead up to St. Aubert's death introduces several of the key "mysteries" alluded to in the novel's title, and means that Emily will have to wrestle with trying to understand his legacy, and her own family history.