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In 1564 several bodies of commissioners were appointed to visit certain portions of Leinster, Munster, and Connaught to enforce the Acts of Supremacy and Uniformity, and about the same time a royal proclamation was issued enforcing the fine of twelve pence for each offence on those who refused to attend Protestant service on Sundays and holidays. Whether these commissioners acted or not is not clear, but undoubtedly the commissioners appointed for the Pale made a serious attempt to carry out their instructions. They brought together juries chosen out of the parishes situated within the sphere of English influence "and upon the return of their several verdicts they found many and great offences committed against her Majesty's laws and proceedings. But among all their presentments they brought nothing against the nobility and chief gentlemen, who yet have contemned her Majesty's most godly laws and proceedings more manifestly than any of the rest, and therefore they determined to call them before them, and to minister to them certain articles, unto which they required the nobility to answer upon their honours and duty without oath. The rest of the gentlemen answered upon their oaths. And when they brought their several answers, they found by their own confession, that the most part of them had continually, since the last Parliament, frequented the Mass and other services and ceremonies inhibited by her Majesty's laws and injunctions, and that very few of them ever received the Holy Communion, or used such kind of public prayer and service as is presently established by law." "Whereupon," Loftus added, "I was once in mind (for that they be so linked together in friendship and alliance one with another, that we shall never be able to correct them by the ordinary course of the statute) to cess upon every one of them, according to the quality of their several offences, a good round sum of money, to be paid to your Majesty's use, and to bind them in sure bonds and recognisances ever hereafter dutifully to observe your Majesty's most godly laws and injunctions. But for that they be the nobility and chief gentlemen of the English Pale, and the greatest number too; I thought fit not to deal any further with them until your Majesty's pleasure were therein specially known." So long as her Majesty required the noblemen of the Pale to fight against Shane O'Neill and the other Irish chieftains she was too prudent to insist on strict acceptance of her religious innovations.
In 1560 Pius IV. determined to send a special commissary into Ireland in the person of the Irish Jesuit, Father David Wolf, who was a native of Limerick, highly recommended to the Holy See by the general of the Society. The commissary was instructed to visit and encourage the bishops, clergy, and chief noblemen of the country to stand firm; he was to draw up lists of suitable candidates for bishoprics, to re-organise some of the religious houses and hospitals, and to establish grammar schools where the youth of the country might receive a sound education. He left Rome in August 1560, and arrived in Cork in January 1561. According to his report the people flocked to him in thousands to listen to his sermons, to get absolution, and to procure the re-validation of invalid marriages. For so far, he was able to assure the Roman authorities, heresy had made no progress among the masses. From Cork he went to Limerick, and from Limerick he journeyed through Connaught. During the course of this journey he learned a great deal that was favourable about Bodkin the Archbishop of Tuam and Roland De Burgo of Clonfert. He visited the greater part of the country with the exception of the Pale, and, as he found it impossible to go there, he empowered one of the priests to absolve from reserved cases, particularly from the crimes of heresy and schism. In 1568 he was arrested and thrown into prison together with Archbishop Creagh of Armagh. Pius V. instructed his nuncio in Spain to request the good offices of Philip II. to procure their release, but apparently the representations of the Spanish government were without effect. In 1572, however, Father Wolf succeeded in making his escape from prison, and before setting sail for Spain he had the happiness of receiving the humble submission of William Casey, who had been promoted to the See of Limerick by Edward VI. From Tarbet the papal commissary sailed for Spain. Later on he returned once more to Ireland, and was active in assisting James Fitzmaurice. He is supposed to have died in Spain in 1578 or 1579.
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/, 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. 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.
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. 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.
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, 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, 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. By his disappearance the power of the Irish in Ulster was broken, and the way was at last prepared for subduing the northern portion of Ireland.
In the South of Ireland the young Earl of Desmond was in a particularly strong position, but, unfortunately, he was personally weak and vacillating, and by playing off the Earl of Ormond against him Elizabeth was able to keep him in subjection to England, to use him against Shane O'Neill, and to prevent him from taking part in a national or religious confederation. In 1567 the Earl was arrested and sent to London, where he was detained as a prisoner. Although the Lord Deputy allowed himself to be received at Limerick by Bishop Lacy with full Catholic ceremonial, still the appointment of Protestant commissioners to administer the territories of Desmond, and the intrusion of a queen's archbishop into the See of Cashel (1567) made it clear that the government was determined to force the new religion on the people. About the same time the Pope took steps to strengthen the Catholics of Munster by appointing Maurice Fitzgibbon, commendatory abbot of a Cistercian monastery in Mayo, to the vacant See of Cashel. The new archbishop was in close correspondence with the Desmond party in Ireland, and with Philip II. of Spain. On his arrival in Ireland (1569) he found that James Fitzmaurice, the cousin of the Earl of Desmond, was organising a confederation to defend the Catholic religion. MacCarthy Mor, the O'Briens of Thomond, the sons of the Earl of Clanrickard, and Sir Edmund Butler had promised their assistance. The new archbishop came to Cashel, took possession of his cathedral in spite of the presence of the royal intruder, and even went so far as to force the latter to attend a solemn Mass in the cathedral. This is the only foundation for the story that he suffered personal violence to MacCaghwell or that he captured him and brought him a prisoner to Spain.
The Earl of Sidney mustered his forces to proceed against the rebels, and the Earl of Ormond was sent over from England to detach his brother Sir Edmund Butler from his alliance with the Desmonds. The Archbishop of Cashel was dispatched into Spain to seek the assistance of Philip II. (1569), and he brought with him a document purporting to be signed by thirteen archbishops and bishops, and by most of the leading Irish and Anglo-Irish nobles in Leinster, Munster, and Connaught, asking the King of Spain to assist them in their defence of the Catholic religion, and offering to accept as their sovereign any Spanish or Burgundian prince whom Philip II. might wish to nominate. The fact that the Pope had published in February 1570 the Bull, /Regnans in excelsis/ announcing the excommunication and deposition of Queen Elizabeth served to encourage the Catholics of Munster, but notwithstanding this sentence the archbishop failed to obtain any effective assistance either from Spain or from the Pope. Undaunted by the ill-success of his agent, Fitzmaurice issued a proclamation addressed to the prelates, princes, and lords of Ireland, announcing that he had taken up arms against a heretical ruler who had been excommunicated and deposed by the Pope, that a large body of English Catholics were in rebellion or were ready to rise, that he had been appointed by the Pope captain-general of the Irish Catholic forces, and that it behoved them to rally to his standard to defend the Catholic faith, to suppress all false teachers and schismatical services, and to deliver their country from heresy and tyranny. Fitzmaurice was, however, disappointed in his hopes. The Earl of Ormond hastened over to Ireland to hold the Butler territories for the queen. Many of his confederates deserted him or were overthrown, and after a long struggle he was overcome and obliged to make his submission (1573-74).