As Giovanni begins to suspect that Beatrice is poisonous, Hawthorne uses the motif of natural vs. unnatural to trace Giovanni's mounting horror. Giovanni is afflicted with a mixture of conflicting emotions:
It was not love, although her rich beauty was a madness to him; nor horror, even while he fancied her spirit to be imbued with the same baneful essence that seemed to pervade her physical frame; but a wild offspring of both love and horror that had each parent in it, and burned like one and shivered like the other[...] Blessed are all simple emotions, be they dark or bright! It is the lurid intermixture of the two that produces the illuminating blaze of the infernal regions.
What the story condemns about Rappaccini is the way he disturbs the natural order by cross-breeding plants to produce species that do not exist in nature—all for the purpose of satisfying his greed for knowledge. Like these artificial bodies, Giovanni’s feelings toward Beatrice are the unnatural “offspring” of love and horror: his suspicions that she might be poisonous corrupt his love for her.
Another form of “wild offspring” in the story is Beatrice herself. Just as Rappaccini produces artificial plant species, he also manipulates human anatomy in the form of his own daughter. The story repeats, in various forms, the notion that Beatrice’s poisonous anatomy transgresses the natural order. As Baglioni introduces his supposed antidote for her condition, he declares, “Possibly we may even succeed in bringing back this miserable child within the limits of ordinary nature, from which her father’s madness has estranged her.” Baglioni's comment implies that Rappaccini's experimentation has placed Beatrice in the realm of the unnatural, beyond the pale of daily life. In this way, the story suggests that there are boundaries to knowledge-seeking that humanity should not cross.
The story uses the motif of alienation in order to convey the destructive impact of Rappaccini's experiment. The narrator repeatedly emphasizes the "solitude" of the garden, most significantly when Giovanni and Beatrice discover that he, too, has become poisonous:
They stood, as it were, in an utter solitude, which would be made none the less solitary by the densest throng of human life.
By making Giovanni and Beatrice poisonous, Rappaccini estranges them from the rest of society. Indeed, they are plunged in "an utter solitude" that isn't just situational—even if there were "throng[s]" of people alongside them in the garden, they would still be isolated and alienated because of their poisoned condition.
As Beatrice lies on her deathbed, Rappaccini defends his experiment: the poison, he claims, has endowed Beatrice with "marvellous gifts against which no power or strength could avail an enemy." For him, Beatrice's poison gives her protection and power. Yet Beatrice declares that she "would fain have been loved, not feared." Although her poison protects her, it alienates her from others. In similar fashion, Rappaccini's scientific pursuits estrange him from society: he "cares infinitely more for science than for mankind" and is willing to sacrifice human life to acquire new knowledge. Through this motif, the story shows that manipulating nature for the sake of science comes at a cost to human togetherness.
Through its depiction of Giovanni's internal conflict surrounding the question of whether Beatrice is good or evil, the story establishes a motif that pits reason against intuition. Giovanni's gut feeling—that is, his intuition—tells him that Beatrice is just as good and pure as she appears, yet he is plagued by rational doubt, as he worries and suspects that she is colluding with her father to poison him. When he discovers that he has become poisonous through proximity to Beatrice, he makes hurtful claims about her moral character, and these claims ultimately destroy their relationship, since they reveal his suspicion of her and suggest that he sees her as a malicious person. By allowing his rational assessment of Beatrice to override both his intuition that she is good and his love for her, Giovanni effectively engineers his own downfall.
Beatrice's final question—"Oh, was there not, from the first, more poison in thy nature than in mine?"—suggests that the so-called "reason" Giovanni uses to accuse her is actually more toxic than anything she has done. Indeed, Giovanni's suspicions might seem rational, but they've really only given him an excuse to doubt his relationship with Beatrice. In this way, he has allowed his impulse toward reason to poison his and Beatrice's romance.
The narrator's descriptions of Rappaccini's garden often portray the poisonous plants as if they are people. This use of personification sheds light on the idea that Rappaccini uses elements of the natural world in unnatural ways. When Giovanni sees the garden for the first time, the story includes the following observation:
The strange plants were basking in the sunshine, and now and then nodding gently to one another, as if in acknowledgement of sympathy and kindred.
In this description, the plants are presented as a sort of community, as if they enjoy each other's presence while also empathizing with each other. This, in turn, implies that there's something about their situation that is unfavorable or upsetting. They "bask in the sunshine," but they also feel a certain "sympathy" for one another, almost suggesting that they're somehow unhappy to be part of Rappaccini's garden. There's an implication, then, that nature itself has no interest in the malicious intentions of someone like Rappaccini, even if the plants are technically poisonous. After all, certain plants are poisonous for reasons of self-protection, which ultimately have nothing to do with the twisted experiments Rappaccini wants to the plants for. By personifying these plants, then, the story underscores the idea that what's truly unnatural about Rappaccini's garden isn't that it contains poisonous plants, but that he intends to use them to carry out twisted experiments on humans in the name of science.