As the plot unfolds, several other people mysteriously die. The protagonists explore a labyrinthine medieval library, the subversive power of laughter, and come face to face with the Inquisition. It is left primarily to William's enormous powers of logic and deduction to solve the mysteries of the abbey.
On one level, the book is an exposition of the scholastic method which was very popular in the 14th century. William demonstrates the power of deductive reasoning, especially syllogisms. He refuses to accept the diagnosis of simple demonic possession despite demonology being the traditional monastic explanation. Despite the abbey being under the misapprehension that they are experiencing the last days before the second coming of Christ (a topic closely examined in the book), William, through his empirical mindset, manages to show that the murders are, in fact, committed by a more corporeal instrument. By keeping an open mind, collecting facts and observations, following pure intuition, and the dialectic method, he makes decisions as to what he should investigate, exactly as a scholastic would do. However, the simple use of reason does not suffice. The various signs and happenings only have meaning in their given contexts, and William must constantly be wary of which context he interprets the mystery. Indeed, the entire story challenges the narrator, William's young apprentice Adso, and the reader to continually recognize the context he is using to interpret, bringing the whole text to various levels which can all have different hermeneutical meanings. The narrative ties in many varied plot lines, all of which consider various interpretations and sources of meanings. Many of the interpretations and sources were highly volatile controversies in the medieval religious setting, all while spiraling towards what seems to be the key to understanding and truly interpreting the case. Although William's final theorems do not exactly match the actual events as written, those theorems do allow him to solve the abbey's mystery.
Eco uses the process of solving the murders as an extended metaphor for a reader’s experience of interpreting a text. William’s search for the truth is a reflection of Post-modernist ideas on the relativistic nature of truth and meaning in this process. The various signs and events in The Name of the Rose only have meaning in their given contexts, and William must constantly be wary of which context is relevant when he interprets the mystery. Though William's final theories do not exactly match the actual events, they allow him to solve the abbey's mystery and thus attain a measure of truth.
Eco wrote that during the Middle Ages there was a conflict between "a geometrically rational schema of what beauty ought to be, and the unmediated life of art with its dialectic of forms and intentions". Eco uses several dialogues and events to link these ideas with the desire to resolve the seeming conflict of structured religion with the spirituality. He sets up several parallel philosophical conflicts within the novel: absolute truth vs. individual interpretation, stylised art vs. natural beauty, predestination vs. free will, spirituality vs. religion.
Eco also translates these medieval religious controversies and heresies into modern political and economic terms. This gives the reader a modern context to help them come to their own conclusions about the meaning of the novel and the views of the characters.
Eco, being a semiotician, is hailed by semiotics students who like to use his novel to explain their discipline. The techniques of telling stories within stories, partial fictionalization, and purposeful linguistic ambiguity are prominent in Eco's narrative style. The solution to the central murder mystery hinges on the contents of Aristotle's book on Comedy, of which no copy survives; Eco nevertheless plausibly describes it and has his characters react to it appropriately in their medieval setting, which, however, though realistically described, is partly based on Eco's scholarly guesses and imagination. It is virtually impossible to untangle fact / history from fiction / conjecture in the novel.
Umberto Eco is a significant postmodernist theorist and The Name of the Rose is a postmodern novel. For example he says in the novel "books always speak of other books, and every story tells a story that has already been told." This refers to a postmodern ideal that all texts perpetually refer to other texts, rather than external reality. In true postmodern style, the novel ends with uncertainty: "very little is discovered and the detective is defeated" (postscript). William of Baskerville solves the mystery by mistake; he thought there was a pattern but it was all in fact accidental. Thus Eco has turned the modernist quest for finality, certainty and meaning on its head leaving the overall plot simply one of accident and without meaning. Even the novel's title is without meaning, Eco saying in the Postscript he chose the title "because the rose is a symbolic figure so rich in meanings that by now it hardly has any meaning left."
The book's last line, "Stat rosa pristina nomine, nomina nuda tenemus" translates literally as "Yesterday's rose endures in its name; we hold empty names". It can also be translated more roughly as "Of the rose of the past, we have only its name". The general sense, as Eco pointed out, was that from the beauty of the past, now disappeared, we hold only the name. In this novel, the lost "rose" could be seen as Aristotle's book on comedy (now forever lost), the exquisite library now destroyed, or the beautiful peasant girl now dead. We only know them by the description Adso provides us — we only have the name of the book on comedy, not its contents. Perhaps this is a deliberate mis-translation. This quote has also been translated as "Yesterday's Rome stands only in name; we hold only empty names."
As Adso points out at the end of the fifth day, he does not even know the name of the peasant girl to lament her. Does this mean she does not endure at all? This line is a verse by twelfth century monk Bernard of Cluny (also known as Bernard of Morlaix). Medieval manuscripts of this line are not in agreement; Eco quotes one Medieval variant verbatim, Eco was not at the time aware of the text more commonly printed in modern editions, in which the reference is to Rome (Roma), not to a rose (rosa). The alternative text, with its context, runs: Nunc ubi Regulus aut ubi Romulus aut ubi Remus? / Stat Roma pristina nomine, nomina nuda tenemus. This translates as "Now where is Regulus, or Romulus, or Remus? / Yesterday's Rome stands only in name; we hold empty names.
As usual in Eco's novels, there is a display of erudition. The blind librarian Jorge from Burgos is a pun on Argentinian writer Jorge Luis Borges, a major influence on Eco. Borges was blind during his later years and was also director of Argentina's national library; his short story "The Library of Babel" was a clear inspiration for the secret library in Eco's book: "The Library is composed of an indefinite, perhaps infinite, number of hexagonal galleries, with enormous ventilation shafts in the middle, encircled by very low railings." Another one of Borges's stories, "The Secret Miracle" features a blind librarian. In addition, a number of other themes drawn from various of Borges's works are used throughout The Name of the Rose: labyrinths, mirrors, sects and obscure manuscripts and books.
Eco spent some time at the University of Toronto while writing the book. The stairs in the monastery's library bear a striking resemblance to those in Robarts Library. Throughout the book, there are Latin quotes, authentic and apocryphal. There are also discussions of the philosophy of Aristotle and of a variety of millenarist heresies, especially those associated with the fraticelli. Numerous other philosophers are referenced throughout the book, often anachronistically, including Wittgenstein. The "poisoned page" theme is in a classic Chinese novel Jin Ping Mei, usually translated into English as The Golden Lotus.
The book describes monastic life in the 14th century. The action takes place at a Benedictine abbey during the controversy surrounding the Apostolic poverty between branches of Franciscans and Dominicans; see Renewed controversy on the question of poverty. The Spirituals abhor wealth, bordering on the Apostolics or Dulcinian heresy. The book highlights this tension that existed within Christianity during the medieval era: the Spirituals, one faction within the Franciscan order, demanded that the Church should abandon all wealth, and some heretical sects began killing the well-to-do, while the majority of the Franciscans and the clergy took to a broader interpretation of the gospel.
A number of the characters, such as the Inquisitor Bernard Gui and the Minorite Michael of Cesena, are historical figures, though the novel's characterization of them is not always historically accurate. However, Eco notes in a companion book that he had to site the monastery in mountains so it would experience early frosts, in order for that action to take place at a time when Bernard Gui could have been in the area. For the purposes of the plot, he needed a quantity of pig blood, but at that time pigs were not usually slaughtered until a frost had arrived. Later in the year Gui was known to have been away from Italy and could not have participated in the events at the monastery.