The chief suspect for these deaths, William asserts, is the library assistant Berenger. But there is more to the mystery than the series of deaths, for further probes inside the library unravel great hidden secrets that could embarrass and topple Christian authority over the masses. The intrigue and the suspense intensify as further evidence and events unfold, leading to a gripping climax and ending.
The books in the library are the special significance to the plot and substance of the movie. It is suggested by William early in his investigation that notes and translation to the Greek version of a book are found on the desk of Venantius. And later during the investigations of the library, he discovers invaluable collections of ancient wisdom, including such Greek luminaries as Aristotle, Plato, Socrates, etc. The Abbott and the institution of Church would not be pleased upon learning of this discovery, for this ancient wisdom is more sophisticated than what is found in the Holy Bible. More importantly, that such wisdom could emanate from Pagan worshippers such as the ancient Greeks would undermine the authority of Christian theologians in Medieval Europe. Considering all these potential threats to their power and privilege, the presence of these books in the hidden library has been kept a tightly held secret. And attempts to crack open its access points are what sets up the central plot of the story. Hence, the books and the secret library containing them are central to the narrative.
The message to be gathered from this story is rather discouraging. Authority figures usually tend to act brutally and ruthlessly in suppressing dissenting voices and views.