It was part of the Vatican's accumulation of items they deemed unwise for the general public to know about, along with the Collection of Necessary Secrets and the Crow Gallery. (PROSE: Christmas on a Rational Planet)
The library was hidden in St Giles Rookery area of Holborn, London so that the Vatican could deny its existence. The books in the library had been hidden by the church for the protection of the public; a small number of patrons were allowed access to the library, but with very few exceptions the books had to stay on the premises. Anyone caught attempting to remove a book had their hands cut off.
Specific works included the journal of Redvers Fenn-Cooper, (PROSE: All-Consuming Fire) Ludwig Prinn's De Vermis Mysteriis, (PROSE: White Darkness) texts referring to the legend of Zagreus, (AUDIO: Zagreus) The Gnostic Apocrypha of Nostradamus, (PROSE: Millennial Rites) and Love's Labour's Won (PROSE: The Empire of Glass).
The unprecedented theft of a book from the library in 1887 led the church to enlist the aid of Sherlock Holmes, who soon discovered that book was last read by the Seventh Doctor. (PROSE: All-Consuming Fire)
In the 20th century, Professor Travers was granted access to the library when researching possible previous invasion attempts by the Great Intelligence. Both the Professor's daughter Anne and Ashley Chapel used books from the library in 1999 to learn quantum mnemonics, the language of the Old Ones. The Doctor, in an incarnation prior to the Sixth Doctor, also visited the library while investigating these events. By this time it appeared that Chapel had purchased the Library from the Vatican. (PROSE: Millennial Rites)
The Doctor once successfully borrowed several books from the Library and brought them to TARDIS' library. When he found them in his fifth incarnation, he realised he still had to return them. (AUDIO: No Place Like Home)