Not only did the archbishop not take any part in the political measures of the Ulster chieftain, who was often at war with Elizabeth, but he soon came to a disagreement with him on purely conscientious grounds, and finally excommunicated him. In the midst of the many difficulties which surrounded him, he resolved to inculcate peace and loyalty to Elizabeth throughout Ulster, asking of Shane only one favor, that of founding colleges and schools, and thinking that, by remaining loyal to the queen, he might obtain her assistance in founding a university. The good prelate little knew the character of the woman with whom he had to deal, imagining probably that the decree of her spiritual supremacy would remain a dead letter for the priesthood, as had been falsely promised to the laity. But he was not left long to indulge in these delusions; for, in the act of celebrating mass in a monastery of his diocese, he was betrayed by some informer, and was arrested by a troop of soldiers, who conducted him before the government authorities, by whom he was sent to London and confined in the Tower on January 18,1565. He was there several times interrogated by Cecil and the Recorder of London, who could easily ascertain that the prelate was altogether guiltless of political intrigue. He escaped miraculously, passed through Louvain, went to Spain, at the time at peace with England, and, wishing to return to Ireland, wrote, through the Spanish ambassador, to Leicester, then all-powerful with the queen, to protest beforehand that, if the Pope should order him to return to his diocese, he intended only to render to Caesar what is Caesar's and to God what is God's. Even then, after his prison experience of several months, he thought that, if he could persuade Elizabeth that he was truly loyal to her, she would forgive him his Catholicity. Receiving no answer, he set sail for his country, where he landed in August, 1566, and shortly after wrote to Sir Henry Sidney, then lord-deputy, in the very terms he had used with Leicester, and proposing in addition to use his efforts in inducing Shane O'Neill to conclude peace. What Sidney and his masters in London, Cecil and Leicester, must have thought of the simplicity of this good man, it is impossible to say. They condescended to return no answer to his more than straightforward communication, save the short verbal reply concerning O'Neill: "We have given forth speach of his extermination by war." The good prelate, after having so clearly defined his position, thought he might safely follow the dictates of his conscience, and govern his flock in peace; but he was soon taken prisoner, in April, 1567, by O'Shaughnessy, who received a special letter of thanks from Elizabeth for his services on this occasion.