Grenouille is born in a market in Paris in July of 1738 to a young fishmonger. Due to the heat and the stench, Grenouille’s mother passes out immediately after his birth, drawing a crowd. When she comes to she abandons her baby, but a crowd discovers the baby and his mother is arrested, tried, and beheaded. Grenouille goes through a series of wet nurses, all of whom accuse him of being especially greedy for milk. His final wet nurse is Jeanne Bussie. Several weeks after she takes custody of him, she returns him to Father Terrier at the cloister of Saint Merri, stating that Grenouille is possessed by the devil because he doesn't have a smell. Father Terrier attempts to pay Jeanne Bussie more money to keep the baby but eventually gives in. When the sleeping Grenouille wakes and sniffs the air in a menacing way, Father Terrier is terrified and takes Grenouille straight to Madame Gaillard, who runs a home for orphans.
Madame Gaillard was hit across the face with a poker as a child and as such, has no sense of smell and doesn't experience emotions. She doesn't realize that Grenouille doesn't smell and doesn't expect him to express emotion, which suits Grenouille well. The other children attempt to murder him but eventually give up. As he grows, Grenouille catalogues every scent he comes across. He finds language inadequate to express his olfactory world, and never fully grasps concepts such as morality or goodness. At age eight, the cloister stops paying for Grenouille's keep, and Madame Gaillard sells him to a tanner named Grimal.
Grimal treats Grenouille like an animal and locks him in a closet at night to sleep. Grenouille contracts anthrax and survives the ordeal, which turns him into a valuable worker as he cannot be reinfected, and he's given a bed and a blanket. At 12, Grimal begins to let Grenouille have an evening per week to himself. Grenouille takes the opportunity to traverse Paris and track scents, and feels free for the first time.
One night, while the city of Paris is setting off fireworks in honor of the king, Grenouille catches a whiff of scent that he finds intoxicating. He tracks it to a young teenage girl in the rue de Marais, sitting in a courtyard pitting plums. He strangles her, rips her dress off, and lies with her until her scent is gone. Later that night as he lies in bed, he begins to catalogue his scents into good and bad.
Giuseppe Baldini is an elderly perfumer whose business is going downhill. He's been tasked with impregnating skins for a count with the perfume Amor and Psyche by his rival, Pélissier, and rather than purchase the perfume, he wishes to copy it. After two hours of trying to ascertain the different ingredients, Baldini gives up and decides to sell his business and move to Messina. Then he hears the servant's bell ring, and when he answers the door, it's Grenouille delivering the skins from Grimal. This is the first time that Grenouille has been in a perfumer's shop, and he asks Baldini to take him on as an apprentice. When Baldini scoffs at the idea, Grenouille says that he can create Amor and Psyche. Baldini grants Grenouille the opportunity to mix the perfume. Grenouille's technique is offensive to Baldini, but when Baldini finally yells for Grenouille to stop, he smells Amor and Psyche. Baldini, awestruck, allows Grenouille to make the perfume better and as Grenouille leaves, Baldini says he'll think about taking on Grenouille.
The next day Baldini purchases Grenouille's service from Grimal. Grimal gets very drunk as he celebrates what he thinks is the best deal of his life. While drunk, he slips and drowns in the Seine. Grenouille sets to work creating a number of fantastic perfumes for Baldini, and Baldini's business grows. Baldini teaches Grenouille how to use the alembic to distill herbs and spices, and once Grenouille has a grasp of the process, Baldini allows him to distill other items. When Grenouille fails to create the scent of doorknobs or water using the distilling process, he falls deathly ill and is diagnosed with syphilitic measles. Baldini is distraught, as he is planning to expand his business and needs Grenouille to do so. Finally, Grenouille asks Baldini about other methods of extracting scent. Baldini explains that there are several other methods, all superior to distillation, and the town of Grasse is the capital of these processes. Grenouille then miraculously recovers.
Three years later, Baldini has risen to international fame with his perfumes and he grants Grenouille journeyman's papers and allows him to leave his service. He makes Grenouille promise to never recreate his perfumes and never to return to Paris, which Grenouille agrees to. That night, Baldini's shop, which sits on a bridge, falls into the river, drowning Baldini and his wife.
As Grenouille travels towards Grasse, he finds the purer air outside the city very welcoming, and grows more and more sensitive to the scent of humans. He begins to seek solitude, traveling only at night, and eventually finds himself at a volcano in the most remote region of France. When Grenouille realizes he's completely alone, he decides to stay. He finds a cave big enough to sleep in and a small stream of water, and stays there for seven years. He spends his days daydreaming in his inner palace, sowing pleasant scents during the day and sipping the scent of the girl from the rue de Marais at night. One day, Grenouille suffers a terrible dream in which an oppressive fog of Grenouille's personal smell attempts to suffocate him, and he realizes he has no scent. Disturbed and terrified, Grenouille sets about attempting to ascertain if he indeed has no scent. He discovers that he is scentless and leaves the mountain.
Grenouille encounters humanity in a small village, where his story that he was abducted by robbers and kept in a cave is brought to the attention of the marquis de la Taillade-Espinasse, who developed the theory of fluidium vitale/letale. The theory states that gases in the earth are poisonous, while gases from "earth removed" regions are healing. Grenouille proves a perfect subject for study, and the marquis makes Grenouille a subject of a lecture he gives and also has Grenouille eat purifying foods for a week and gives him new clothes. Grenouille finds that he looks extremely normal. One day, when the marquis attempts to dust him with violet perfume, Grenouille stages a fainting spell and tells the marquis that the perfume is from the earth and poisonous. The marquis contacts a local perfumer and Grenouille is allowed to use his shop to create a new perfume. The perfume Grenouille creates is a faux human scent. He decides to test it in the town and finds that the townsfolk regard him as a normal person now that he smells. Grenouille feels like a genius.
The marquis' next lecture is a sensation, as Grenouille's perfume garners sympathy from the audience. A few weeks later, Grenouille departs the city and heads for Grasse. While wandering the city, he comes across a scent very much like the girl from the rue de Marais, and Grenouille decides he must possess this scent. He finds employment under Madame Arnulfi and her journeyman Druot, and in their shop he learns how to obtain scent from flowers using animal fat.
Over the winter, Grenouille begins to experiment and creates several human-scented perfumes for himself. He's also able to successfully create a perfume of a brass doorknob. He moves on to animals, but finds that he must kill them before he can be successful. Finally he moves onto human subjects by placing small pieces of oily cloth in public places, which soak up human scent and creates the perfume of people.
Dreaming one night about the scent of the girl in the garden, Grenouille suffers the unpleasant thought that even if he does possess her scent, it will eventually run out. He decides that to make it go further, he needs to create a mixed perfume rather than use her scent in its concentrated form. That spring and summer, 24 beautiful young girls in Grasse are systematically murdered by a blow to the head, and are then stripped of their clothes and have their hair shaved off. Terror erupts in the town, especially when it's discovered that the girls are virgins. The murders only stop after the bishop in the town excommunicates the unknown murderer.
Antoine Richis, a widower and the second consul of Grasse, doesn't trust that this peace will last, and doesn't believe the rumors that the murderer has moved on to the nearby Grenoble. His daughter, Laure, has just turned 16 and is immensely beautiful. After a nightmare in which Laure is murdered by the serial murderer, Richis decides that she must be a target still for the murderer. He immediately makes plans to smuggle Laure out of the city and marry her off, as then she'd be protected by having lost her virginity.
Richis and Laure leave early that morning. Grenouille, meanwhile, had been preparing to take Laure's scent that night. But when he steps outside, he finds he cannot smell her and panics. Druot in passing mentions that Richis and Laure left for Grenoble.
Grenouille packs his supplies and tracks the runaways. When he reaches La Napoule, he comes to an inn where Richis and Laure are sleeping. He convinces the innkeeper to let him sleep in the barn. That night, Grenouille creeps in through Laure's window, clubs her, and wraps her in his oil-drenched cloth to steal her scent. He sits and watches her for hours. At daybreak, he unrolls her, packages up the cloth with her scented oil, and leaves. Antoine Richis discovers her body later that morning.
Several days later, Grenouille is arrested. The police find the hair and dresses of the 25 victims in Grenouille's cabin and display this evidence in the church square. His trial proceeds quickly and he's sentenced to death. The parade grounds are prepared for the execution and citizens prepare as though for a holiday. On the day of the execution, the grounds fill with thousands of people, and Grenouille is brought in a carriage to protect him from a mob. As Grenouille exits the carriage, he is wearing the perfume he made from the 25 virgins he murdered, and the crowd is gripped with the thought that Grenouille cannot possibly be a murderer. The effect of Grenouille's perfume then incites an orgy. Grenouille feels like a god, but soon his glee descends into disgust for humans and he begins to faint. Antoine Richis runs to Grenouille. When Grenouille wakes later, he finds himself in Laure's bed and Richis asks Grenouille to be his son. The verdict has been overturned, and Druot is arrested and executed for the murders.
Grenouille travels back to Paris, thinking that he wants to die. When he arrives after midnight, he walks to the Cimetière des Innocents, where vagabonds are gathered. He joins the group and then pours his last bottle of perfume over himself. The group converges on Grenouille and attacks him, tearing his body to bits and eating it. When Grenouille is gone, the group is embarrassed, but everyone feels like they have finally done something out of love.