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Father Wolf had been instructed specially to recommend to the Holy See those priests whom he deemed qualified for appointment to vacant bishoprics. This was a matter of essential importance, and as such he devoted to it his particular care. Thomas O'Herlihy was appointed to Ross (1561); Donald McCongail or Magongail, the companion of his journeys, was appointed to Raphoe (1562); the Dominicans O'Harte and O'Crean were provided to the Sees of Achonry and Elphin in the same year at his request, and during the time he remained in Ireland his advice with regard to episcopal nominations was followed as a rule. He was instructed also to establish grammar schools throughout the country, and he was not long in Ireland till he realised the necessity of doing something for education, and above all for the education of candidates for the priesthood. In 1564 he obtained from Pius IV. the Bull, /Dum exquisita/,[60] empowering himself and the Archbishop of Armagh to erect colleges and universities in Ireland on the model and with all the privileges of the Universities of Paris and Louvain. For this purpose they were empowered to apply the revenues of monasteries, and of benefices, and to make use of the ecclesiastical property generally. Unfortunately owing to the disturbed condition of the country, and the subsequent arrest of both the archbishop and the papal commissary, it was impossible to carry out this scheme.

In the earlier sessions of the Council of Trent the Archbishop of Armagh had taken a leading part. When the Council opened for its final sessions in January 1562 Ireland was represented by O'Herlihy of Ross, McCongail of Raphoe, and O'Harte of Achonry. Nor were these mere idle spectators of the proceedings. They joined in the warm discussions that took place regarding the Sacrifice of the Mass, Communion under both kinds, the source of episcopal jurisdiction and of the episcopal obligation of residence, the erection of seminaries, and the matrimonial impediments. It is said that it was mainly owing to their exertions that the impediment of spiritual relationship was retained.[61] After their return attempts were made to convoke provincial synods to promulgate the decrees of the Council of Trent.

In 1566 apparently some of the prelates of Connaught assembled and proclaimed them in the province of Tuam; in 1587 the Bishops of Clogher, Derry, Raphoe, Down and Connor, Ardagh, Kilmore, and Achonry, together with a large number of clergy met in the diocese of Clogher for a similar purpose, and in 1614 they were proclaimed for the province of Dublin by a synod convoked at Kilkenny.[62]

In 1560, and for several years after, the state of affairs in Ireland was so threatening that Elizabeth and her advisers were more concerned about maintaining a foothold in the country than about the abolition of the Mass. In the North Shane O'Neill had succeeded on the death of his father (1559), and seemed determined to vindicate for himself to the fullest the rights of the O'Neill over the entire province of Ulster. The Earl of Kildare refused to abandon the Mass, and was in close correspondence both with his kinsman the Earl of Desmond, and with several of the Irish chieftains. It was feared that a great Catholic confederation might be formed against Elizabeth, and that Scotland, France, Spain, and the Pope might be induced to lend their aid.[63] Instructions were therefore issued to the Lord Deputy to induce the Earl of Kildare to come to London where he could be detained, and to stir up the minor princes of Ulster to weaken the power of O'Neill. By detaining men like the Earls of Kildare, Desmond, and Ormond in London, by stirring up rivalries and dissensions amongst Irishmen, and above all by getting possession of the children of both the Anglo-Irish and Irish nobles and bringing them to England for their education, it was hoped that Ireland might be both Anglicised and Protestantised.[64]

The most urgent question, however, was the reduction of Shane O'Neill.

At first Elizabeth was inclined to come to terms with him, but the Earl of Sussex in the hope of overcoming him by force had him proclaimed a traitor, and advanced against him with a large force (1561). He seized Armagh, took possession of the cathedral, and converted it into a strong fortress. O'Neill soon appeared accompanied by the lawful archbishop, who exhorted the Irish troops to withstand the invader. The English army suffered a bad defeat, and after the failure of several attempts to reduce O'Neill by force, the Deputy determined to try other methods. He hired an individual named Neil Gray to murder O'Neill and acquainted Elizabeth with what he had done,[65] but O'Neill was fortunate enough to elude the assassin. At length O'Neill was induced to go to England (1562), where he was forced to agree to certain terms; but, as he discovered that he had been deceived throughout the entire negotiations, he felt free on his return to assert his claims to Ulster. Elizabeth was not unwilling to yield to nearly all his demands, even to the extent of removing Loftus from the Archbishopric of Armagh and allowing the appointment of O'Neill's own nominee. The Earl of Sussex, however, was opposed to peace. Having been forced, against his will, to come to terms with O'Neill (1563), he determined to have recourse once more to the method of assassination. A present of poisoned wine was sent to O'Neill by the Deputy as a token of his good will,[66] and it was only by a happy chance that O'Neill and his friends were not done to death. The new Deputy, Sir Henry Sidney, succeeded in stirring up O'Donnell and the other Ulster princes against O'Neill by promising them the protection of England. Having been defeated in battle by O'Donnell in 1567, Shane fled for aid to the Scots of Antrim, on whom he had inflicted more than one severe defeat, and while with them he was set upon and slain.