Hawthorne begins the story with a brief description of the literary style and work of fictional Monsieur L'Aubepine, the author of "Rappaccini's Daughter".
Giovanni Guasconti, a young man from southern Italy, comes to Padua to pursue a University education. His room, a high and gloomy chamber in an old mansion, is desolate but for a sole window, which overlooks a beautiful garden. The garden, the youth is told, belongs to Signor Giacomo Rappaccini, a famous doctor who distils the plants from his garden into medicines. In the center of the magnificent garden is one particularly interesting plant – a large shrub with purple blossoms set in a marble vase.
While peering through his window, Giovanni spies the doctor working in the garden. The doctor, a tall, old, emaciated and sickly looking man, examines each plant with clinical intentness; he does not treat the plants with emotion, avoiding both their odors and their touch. As the doctor nears the purple plant, he puts on a mask, but as if finding the task of tending to the plant to be still too dangerous, he calls for his daughter, Beatrice. He relinquishes care of the plant to his daughter, who, as strikingly beautiful as the plants around her, busily begins to tend to the poisonous plant as if it were a sister. That night, Giovanni dreams about Beatrice; in the dream, “flower and maiden were different, and yet the same, and fraught with some strange peril in either shape".
The next day, Giovanni meets with Signor Pietro Baglioni, a professor of medicine and Giovanni’s father’s old friend. He tells Giovanni that Doctor Rappaccini is a brilliant scientist with an objectionable character, as he cares more for science than for mankind and would gladly sacrifice the lives of others for intellectual gain. Baglioni laughs at Giovanni’s interest in Beatrice; while all young men are “wild” about her, few have had the fortune of seeing her. Baglioni suggests that Beatrice has learned at her father's feet and that "she is already qualified to fill a professor's chair". On the way home, Giovanni happens to pass a florist and purchases a bouquet of flowers.
Back in his room, Giovanni sees Beatrice pluck one of the blossoms from the purple shrub. A few drops of moisture from the plant fall upon a passing lizard, killing it instantaneously. Beatrice seems unsurprised, and fastens the poisonous blossom to her bosom. Soon thereafter, Beatrice stops to admire a beautiful insect – which immediately drops dead, seemingly at her breath. Giovanni witnesses these scenes with awe and horror, but scarcely has time to respond before Beatrice sees him spying on her from the window. He throws down the bouquet of flowers; she thanks him, and runs away. As she leaves, Giovanni believes that he sees the flowers already withering in her grasp.
For days after this encounter, Giovanni avoids the window, with feelings of both fear and love alive in his heart. He took to running through the streets, his pace matching the pace of thoughts whirling about in his brain. One day, he is overtaken by Baglioni, who is surprised at his haste. Doctor Rappaccini passes him, and the look in his eye tells Baglioni that Giovanni has become the subject of one of the Doctor’s experiments. Giovanni does not want to accept this possibility, and breaks away from the old professor.
On his way home, Giovanni is stopped by Lisabetta, an old woman who showed him his room when he first moved to the city. Lisabetta leads him to the garden’s secret entryway; for a moment, the thought asses Giovanni’s mind that this might be part of the doctor’s experiment, but it seemed “absolutely necessary” that he continue into the garden.
Inside the garden, Giovanni and Beatrice begin to talk. She mentions that she knows nothing of her father’s science, and asks Giovanni to believe only what he sees with his own eyes. Walking through the garden, they stop at the purple plant. Giovanni extends his hand to pluck one of its blossoms, but Beatrice grasps his hand and flings it away from the plant, exclaiming that it is “fatal”. Beatrice flees, and Giovanni sees the Doctor watching them from the shadows. When Giovanni awoke the next day, his hand in pain from her touch, a purple outline of her fingers visible on his skin.
After many meetings with Beatrice, Giovanni is visited one day by Professor Baglioni, who comments on the smell of a strange perfume in Giovanni’s room. Baglioni tells Giovanni a story of an Indian prince who sent a woman as a present to Alexander the Great. This woman was beautiful, but had a deadly secret – she had been nourished with poison since birth, so that her being became poisonous and her embrace would bring death. Baglioni tells Giovanni that this is Beatrice’s secret as well, a truth Giovanni is unwilling to accept. Baglioni gives Giovanni a vial with an antidote, which he urges Giovanni to give to Beatrice and cure her of her father’s work. After showing his visitor the door, however, Giovanni finds that flowers wilt at his touch, and a spider dies from his breath. He realizes that he has now become poisonous, like Beatrice.
In the garden, he confronts Beatrice about the plant. She reveals that her father created it, and that she knew of its dangerous powers – and of its effect on her. Giovanni curses her for severing him from the world and knowingly entrancing him into the same horrible state. Beatrice is shocked, and gravely upset by this. She swears ignorance, and although Giovanni comes to believe her, his words had already hurt her deeply. Giovanni doesn’t realize the weight of his words and believes he can still save her; he gives her the antidote, which she willingly drinks. At that same instant, her father appears. He tells her that it was nor a curse, but rather a gift, to be made as “terrible” as she was beautiful. But, Beatrice retorts that she would rather have been loved than feared. As she sinks to the ground, she reminds Giovanni of his hateful words, and asks him, “was there not, from the first, more poison in thy nature than in mine?” The poison in her body had become part of her life; the antidote succeeded not in saving her but in killing her. Baglioni, looking forth from the window, is both triumphant for finally defeating Rappaccini at his own game – but also horrified at the result.
Hawthorne begins this story with a preamble about the French "author" of the tale - a man by the name of l'Aubepine. In French, aubepine is the name for a flowering shrub known in English as hawthorn. "Rappacini's Daughter" begins with a literary joke which calls attention to Hawthorne's role as storyteller, and continues with allusions to works such as The Divine Comedy and the Bible. Beatrice, the title character, is a reference to Dante's guide through Paradiso in The Divine Comedy; Giovanni's own relative is rumored to have been the inspiration for one of Dante's characters; Rappaccini's garden is referred to as the "Eden of the present world". Beatrice's undoing at the end of the story is precipitated by her loss of innocence; once she knows that she is poisonous, she chooses to die.
The story’s tragic end demonstrates that Beatrice’s death is the product of the ambitions of three men. Her father, Doctor Rappaccini, may be considered a callous scientist who, as Baglioni would have us believe, offered his daughter up as a scientific experiment. Rappaccini’s true motivations, however, are revealed in his final words to his daughter:
"My daughter, thou art no longer lonely in the world! Pluck one of those precious gems from thy sister shrub, and bid thy bridegroom wear it in his bosom. It will not harm him now! My science, and the sympathy between thee and him, have so wrought within his system, that he now stands apart from common men, as thou dost, daughter of my pride and triumph, from ordinary women. Pass on, then, through the world, most dear to one another, and dreadful to all besides!"
Beatrice, however, laments her condition, to which Rappaccini replies:
"What mean you, foolish girl? Dost thou deem it misery to be endowed with marvellous gifts, against which no power nor strength could avail an enemy? Misery, to be able to quell the mightiest with a breath? Misery, to be as terrible as thou art beautiful? Wouldst thou, then, have preferred the condition of a weak woman, exposed to all evil, and capable of none?"
In these words, Rappaccini demonstrates that he meant not to harm his daughter, but rather protect her from the evils of the world. In a sense, he can be regarded as the most dedicated of fathers, using his ingenuity and expertise to fashion a lasting defense mechanism for his daughter. On the other hand, in his final exchange with Beatrice, he does not seem to understand why his daughter would prefer to live a normal and defense-free human being. Instead, he naively believed that bringing Giovanni into her same state so that the two could live an insulated life together could make her happy. How could such an intelligent scientist misunderstand the needs of the human heart?
Giovanni, too, is not what we originally see. Instead of a youth in love, he is merely overtaken with curiosity, lust, and vanity. In fact, his interest in Beatrice can, in a way, be compared to Rappaccini’s interest in science, and Baglioni’s interest in the old rules of medicine. All these men care for one thing, but in pursuing it, neglect its true foundation. Giovanni rashly lashes out at Beatrice, demonstrating that his love for her was ridden with doubt and distrust, demonstrating his own shallow and selfish nature. Rappaccini aims to protect his daughter, but in doing so, overlooks her personal interests. And Baglioni, while claiming to uphold the good rules of medicine that protect human life, invest suspicions into Giovanni’s mind and presents him with the very “medicine” that kills Beatrice, making him just as evil as Rappaccini in the end.
This story bears a similar lesson to those learned in many of Hawthorne's other works. Specifically, it warns against what may happen to man when, in the quest for scientific or intellectual development, he "attempts to usurp the function of God," a lesson observed in “The Birthmark" and "Ethan Brand". Some have argued that the story is an allegory for the Fall of Man in the Garden of Eden, with Rappaccini as Adam, and Beatrice as Eve. Although in Hawthorne's tale Rappaccini infects Beatrice and not the other way around, the argument has been made that perhaps Hawthorne transferred some of Eve's role to Adam as he did not fully accept the Scriptural description. As is the case with Georgiana in "The Birthmark", Beatrice does not have agency over her own life - only her death. Here, Hawthorne is subtly critiquing the gender roles of his time. Rappaccini and Giovanni's desires to control or change Beatrice lead to her ruin, a fate she accepts.