In 1570 the Papacy had excommunicated Queen Elizabeth I in the bull "Regnans in Excelsis". This had led on to the Second Desmond Rebellion in 1579-83 which was still in progress at the time of his voyage. O'Hurley's voyage was fraught with danger but he was prepared to take the risks involved.
O'Hurley lodged with Baron Thomas Flemyng at Slane, and from there he spread his activities through the territory of the O'Reilly clan. His activities were followed by government spies, and under pain of severe penalties Flemyng was compelled to hand the archbishop into custody. On October 8 1583 O'Hurley was imprisoned in Dublin Castle.
Despite severe torture, which included having his legs boiled over a roaring fire, the Archbishop refused to embrace Protestantism. According to surviving correspondence between Dublin and Whitehall, the Queen was reluctant to dispense with a fair trial under English Law, but her mind was changed by Sir Francis Walsingham and she approved of a trial by military tribunal. O'Hurley was tried in a day and sentenced to death.
On the early morning of Saturday June 20, 1584, O'Hurley was taken outside the walls of Dublin and hanged. In his last speech, he proclaimed his innocence and declared that he died as a martyr for the Roman Catholic Church. He was buried in Saint Kevin's Churchyard. His gravesite remained a site of pilgrimage for many years, but the location has since been lost.
Following Catholic Emancipation in the 19th century, Ireland's Roman Catholic hierarchy began an investigation into his life and death. One of the most valuable resources was found to be the documents and letters written by the men who tortured and executed him. In 1904, he was declared a Servant of God.
"Be it therefore known unto you...that I am a priest anointed and also a Bishop, although unworthy of soe sacred dignitites, and noe cause could they find against me that might in the least deserve the paines of death, but merely for my funcon of priesthood wherein they have proceeded against me in all pointes cruelly contrarie to their own lawes..and I doe injoin you (Deere Christian Brethren) to manifest the same to the world and also to beare witness on the Day of Judgment of my Innocent death, which I indure for my function and profession of the most holy Catholick Faith.--Addressing the crowd which had gathered to watch his execution.