From 1632 till 1640, though the Deputy was doing his best to rob a large portion of the Catholic owners of their property on the ground of defective titles, and though in many districts the Protestant bishops and ministers created considerable difficulties for their Catholic neighbours, still the religious persecution was carried out only in a half-hearted manner. The king was shrewd enough to recognise the important part that might be played by the Irish Catholics in the civil struggle that he foresaw, and he was anxious not to antagonise their leaders. This period of comparative calm was providential for the Church in Ireland, by enabling it to organise its forces and to prepare for the terrible days that were soon to come. In accordance with the advice given by Archbishop Lombard years before, Rome decided to fill several of the Sees that had been left vacant. Hugh MacCaghwell (/Cavellus/), a distinguished Irish Franciscan, who had been instrumental in founding the College of St. Anthony at Louvain, and whose theological works caused him to be regarded by his contemporaries as the ablest theologian of the Scotish school in Europe, was appointed Archbishop of Armagh (1626), but he died in Rome a few weeks after his consecration. Less than two years later it was decided to transfer Hugh O'Reilly from Kilmore to the primatial See (1628). Thomas Fleming had been appointed to Dublin in 1623, and despite the efforts of his enemies he succeeded in eluding the vigilance of those who wished to drive him from Ireland. Malachy O'Queely, who had acted for years as vicar-apostolic of his native diocese of Killaloe, was appointed to Tuam (1630) in succession to Florence Conry, and Thomas Walsh, a native of Waterford, was promoted to the See of Cashel (1626). Amongst the distinguished ecclesiastics who were promoted to Irish dioceses during the reign of James I. and Charles, were the learned David Rothe (Ossory, 1618), Roche MacGeoghan (/Roccus de Cruce/), who had done so much for the restoration of the Dominican houses in Ireland (Kildare, 1629), and Heber MacMahon (Down, 1642, Clogher, 1643). As a result of the long persecution and of the absence of bishops from so many dioceses a certain amount of disorganisation might be detected in several departments, and to remedy this provincial synods were held to lay down new regulations, and to adjust the position of the Church to the altered circumstances of the country. A synod was held at Kilkenny (1627) which was attended by bishops from Leinster and Munster; another very important one, the decrees of which were confirmed by the Holy See, was held for the province of Tuam in 1632, and a third attended by the Leinster bishops was held in the County Kilkenny in 1640. The Irish colleges on the Continent continued to pour able and zealous young priests into the country, while the colleges for the education of the Franciscans, Dominicans, and Jesuits supplied new recruits to replenish the ranks of the religious orders. The Capuchin founded Irish colleges on the Continent, at Lille, Antwerp, and at Sedan, and so earnestly did they work in Ireland that a special letter in praise of the Capuchins was forwarded to Rome by a number of the Bishops in 1642. The results of this renewed activity were soon apparent in every part of the country. Thus, for example, in a report presented (1631) from the diocese of Elphin, then ruled by Bishop Boetius Egan, it can be seen that although all the churches, including the cathedral, had been destroyed or taken possession of by the Protestants, there were at the time forty priests at work in the diocese; the decrees of the Council of Trent had been promulgated; the parishes had been re-arranged, and the learning of the parish priests appointed had been tested by examination; regular synods, visitations, and conferences of the clergy were being held, and steps had been taken to ensure that the people should be instructed fully in their religion.
In the Parliament of 1641 the Catholics were in the majority, and they insisted that the "Graces" must be confirmed. The king granted their demands, and the bill was actually on its way to Ireland when the Lords Justices, Parsons and Borlase, who administered the government of the country prorogued the session. They wished for no settlement with the Catholics lest a settlement might put an end to their hopes of a plantation, and the Earl of Ormond tried also to block the passage of the bill in the hope of saving the king from the odium which he would incur in England and Scotland by granting toleration to the Irish Catholics. The Catholic noblemen of Ireland, whether Irish or Anglo-Irish, had good reason to complain. They had seen the Catholics driven out of the good lands of Ulster to make way for English and Scottish planters, and they well knew that the danger of similar transactions in Connaught, Munster, and Leinster had not passed away with the death of Strafford. They had seen the operation of the Court of Wards, and they could not fail to realise that as a result of its work the landowners of Ireland would soon be dispossessed or Protestantised. They knew something of the Protestant Inquisition courts as run by the ministers and bishops, of the persecution of their clergy, the fees and fines levied on the unfortunate Catholic peasantry, and of the still graver danger that lay before them in case the Covenanters and the Puritans were to overthrow Charles I., or to succeed in forcing him to accept their policy. Were they to remain passive, they believed, they could have no hope of redress or even of safety, and hence many of them made up their minds that the time for negotiations had passed, and that they could rely only on force. Never again were they likely to get such a favourable opportunity. England was torn by internal dissensions; the disbanded Irish soldiers, who had been trained for service against the Scots, were still in the country; and with so many distinguished Irishmen scattered through the countries of Europe there was good hope that they might get assistance from their co-religionists on the Continent. The distinguished Waterford Franciscan, Father Luke Wadding, who had founded the College of St. Isidore in Rome and had taken such a prominent part in the foundation of the Irish College, was in Rome ready to plead the cause of his countrymen at the Papal Court. His fame as a scholar was known throughout Europe, and his active support could not fail to produce its effect in Europe, and particularly in Spain where he was esteemed so highly by Philip IV. Owen Roe O'Neill, who had achieved a remarkable distinction in the army of Spain by his gallant defence of Arras against the French, Colonel Preston, uncle of Lord Gormanston, and a host of others, who had learned the art of war in France, Spain, and the Netherlands, were willing to return to Ireland and to place their swords at the disposal of their country.
Early in 1641 Rory O'More, who was closely connected with both the Irish and the Anglo-Irish nobles, suggested to Lord Maguire of Enniskillen the idea of an appeal to arms, and hinted at the possibility of a union between the Irish nobles and the Lords of the Pale. In a short time most of the important leaders of the North, Sir Phelim O'Neill, Turlogh O'Neill, Lord Maguire, Hugh MacMahon, Arthur MacGennis of Down, Philip and Miles O'Reilly of Cavan had come to an understanding. The war was to begin in Ulster on the night of the 23rd October 1641, and on the same night an attempt was made to seize Dublin Castle. The latter portion of the programme could not be carried out owing to the action of an informer who betrayed Maguire and Hugh MacMahon to the Lords Justices; but at the appointed time the Irish Catholics of Ulster rose almost to a man, and in a very short time most of the strong places in the province were in their hands. In such a movement it was almost impossible for the leaders to prevent some excesses, particularly as many of the men who took part in it had been driven from their lands to make way for the Planters, and had suffered terribly from the harshness and cruelty to which they and their families had been subjected. Naturally they seized their own again, and in some cases they may have used more violence than the situation required, but it is now admitted by impartial historians that the wild stories of a wholesale massacre of Protestants are without any more solid foundation than the fact that the Protestants were for the most part driven out of Ulster in much the same way as the Catholics had been driven to the mountains thirty years before. Most of the few who were killed were probably struck down while attempting to defend their homes, and in no case is there evidence to prove that the leaders countenanced unnecessary violence or murder. If the historian wishes to look for organised lawlessness and murder he can find it much more easily in the campaign of the infamous Sir Charles Coote or in the raids carried out by the forces of the Scotch Covenanters of the North. The Catholic Lords of the Pale hastened to Dublin Castle to offer their services against the Northern rebels, but they were received so discourteously by the Lords Justices that they recognised the absolute necessity of joining with the Catholics of Ulster. In announcing their defection the Lords Justices positively gloated over the splendid prospect of having the province of Leinster planted with English settlers (Dec. 1641). The action of the English Parliament in decreeing that for the future there should be no toleration allowed to Irish Catholics (Dec. 1641) and in putting up for sale two million five hundred thousand acres of fertile land in Ireland, the proceeds to be expended in a war of extermination, strengthened the hands of the Irish leaders, and helped to bring over the waverers to their side.
The Catholic clergy had sympathised with the movement from the beginning, but they had exerted themselves particularly in moderating the fury of their countrymen, and in protecting the Protestants, both laymen and clerics, from unnecessary violence. But, as there was a danger that the movement would break up and that the Irish forces would be divided, it was necessary for the bishops to take action. Religion was nearly the only bond that was likely to unite the Irish and the Anglo-Irish nobles, and the Church was the only institution that could give the movement unity and permanency. A meeting of the bishops and vicars of the Northern province was held at Kells (May 1642) under the presidency of Dr. Hugh O'Reilly, Archbishop of Armagh. They prescribed a three days' fast, the public recitation of the Rosary and the Litanies, and a general Communion for the success of the war, issued a sentence of excommunication against murderers, mutilators, thieves, robbers, etc., together with all their aiders and abettors, denounced the Catholic Irishmen who refused to make common cause with their countrymen, and ordered all bishops, vicars-general, parish priests, and heads of religious houses to spare no pains to raise funds immediately for the support of the soldiers. In May (1642) a national synod was held at Kilkenny. It was attended by the Primate of Armagh, the Archbishops of Tuam and Cashel, by most of the bishops either personally or by procurators, and by representatives of the religious orders and of the secular clergy. They declared that the war was being waged for the defence of the Catholic religion, for the preservation of the rights and prerogatives of the king, for the just and lawful immunities, liberties, and rights of Ireland, for the protection of the lives, fortunes, goods, and possessions of the Catholics of Ireland, and that it was a just war in which all Catholics should join. They condemned murder, robbery, and violence, advised all their countrymen to lay aside racial and provincial differences, took measures for the restoration of the cathedrals and churches to their owners, exhorted all, both clergy and laymen, to preserve unity, and called upon the priests to offer up Mass at least once a week for the success of the war.
During the year 1642 the war had spread into all parts of Ireland, and most of the prominent nobles, with the exception of the Earl of Clanrickard, had taken the field. Owen Row O'Neill and Colonel Preston had arrived with some of the Irish veterans from the Continent, and had brought with them supplies of arms and ammunition. Urban VIII. had forwarded a touching letter addressed to the clergy and people of Ireland (Feb. 1642) and had contrived to send large supplies of weapons and powder. A general assembly of Irish Catholics was called to meet at Kilkenny in October 1642. There were present, eleven spiritual peers, fourteen lay peers, and two hundred and twenty-six representatives from the cities and counties of Ireland, under the presidency of Lord Mountgarrett. Generals were appointed to lead the forces in the different provinces, as unfortunately owing to the jealousy between the Anglo-Irish and the Irish nobles Owen Roe O'Neill could not be appointed commander of the national army. Arrangements were made for sending ambassadors to the principal courts of Europe, for the establishment of a printing-press, for raising money, and for the promotion of education. The Irish Franciscans of Louvain were asked to transfer their press and library to Ireland to help in the creation of a great school of Irish learning. Father Luke Wadding was appointed the Irish representative at the Papal Court, and agents were dispatched to France, Spain, the Netherlands, and to several of the German States. Urban VIII., yielding to the entreaties of the Irish ambassador gave generous assistance, and wrote to nearly all the Catholic rulers of Europe recommending them to assist their co-religionists in Ireland.
In 1643 the well-known Oratorian, Father Francesco Scarampi, landed in Wexford as the accredited agent of the Pope, bringing with him supplies of money and arms. Hardly, however, had he arrived, when he discovered that though the Irish armies had met with considerable success both against the Royalist forces in Dublin and the Scotch Covenanters in the North, negotiations had been opened up for an extended truce. The Anglo-Irish nobles had never been enthusiastic for the war as an Irish war. They fought merely to preserve their estates and to secure a certain degree of liberty of worship, but in their hearts they were more anxious about the cause of the king than about the cause of Ireland. The Marquis of Ormond, whom the king had created his Lord Lieutenant in Ireland, had many friends amongst the Lords of the Pale, and by means of his agents he succeeded in bringing about a cessation (Sept. 1643). The Irish Catholics were to send agents to the king for a full discussion of their grievances, and were to help him with supplies. Anxious to secure the help of the Irish Catholics, and fearing to give a handle to his parliamentary opponents by granting religious toleration, Charles was in a very difficult position, and to make matters worse Ormond was determined not to yield to the demands of the Catholics. He was prepared to make a conditional promise that the laws against them would not be enforced, but beyond that he was resolved not to go.
After long and fruitless negotiations with Ormond the war was renewed (1644). Representatives from France and Spain had arrived in Kilkenny, and it was thought that if the Pope could be induced to send a nuncio such a measure would strengthen the hands of the Irish ambassadors on the Continent. At the request of Sir Richard Bellings, Secretary to the Supreme Council, Innocent X. consented to send Giovanni Battista Rinuccini as his representative to Ireland (1645). The latter landed at Kenmare in October, and proceeded almost immediately to Kilkenny. In the meantime Charles I. was being hard pressed in England, and as he could have no hope of inducing Ormond to agree to such terms as would satisfy the Catholics of Ireland, he commissioned the Earl of Glamorgan, himself a Catholic, and closely connected with some of the Irish families by marriage, to go to Kilkenny and to procure assistance from the Catholic Confederation at all costs. Shortly after his arrival he concluded a treaty in the name of the king (Aug. 1645) in which he guaranteed "the free and public exercise of the Roman Catholic religion." All churches possessed by the Irish Catholics at any time since October 1641 were to be left in their hands, and "all churches in Ireland other than such as are now actually enjoyed by his Majesty's Protestant subjects" were to be given back to the Catholics. All jurisdiction claimed by Protestant bishops or ministers over Irish Catholics was to be abolished, and all temporalities, possessed by the Catholic clergy since October 1641, were to be retained by them, two- thirds of the income, however, to be paid to the king during the continuance of the war. Charles had already addressed a letter to the nuncio promising to carry out whatever terms Glamorgan would concede, and adding the hope that though this was the first letter he had ever written to any minister of the Pope it would not be the last. The terms were to be kept a secret, but in October 1645 Archbishop O'Queely of Tuam was killed near Sligo in a skirmish between the Confederate and Parliamentary forces, and a copy of the treaty which he had in his possession fell into the hands of the enemy. As soon as it was published it created a great sensation in England, and Charles immediately repudiated it. Glamorgan was arrested in Dublin by Ormond, but was released after a few weeks, and returned coolly to Kilkenny to conduct further negotiations.
Since his arrival in Kilkenny (1645) the nuncio was anxious to break off negotiations with Ormond, and to devote all the energies of the country to the prosecution of the war. But the Anglo-Irish of the Pale were bent upon accepting any terms that Ormond might offer; and soon the Supreme Council was divided into two sections, one favouring the nuncio, the other supporting Ormond. Negotiations had been opened directly with Rome by Queen Henrietta through her agent Sir Kenelm Digby. In return for promises of men and money the latter signed a treaty even much more favourable to the Irish Catholics than that which had been concluded with Glamorgan (1645), but as the original of this treaty had not come to hand, and as it was feared that there was little hope of its being put in force, the Supreme Council patched up an agreement with Ormond (March 1646). Although the latter had got a free hand from the king he granted very little to the Catholics. The oath of supremacy was to be abolished in the next Parliament, as were to be also all statutory penalties and disabilities; "his Majesty's Catholic subjects were to be recommended to his Majesty's favour for further concessions;" all educational disabilities of Catholics were to be removed, and all offices, civil and military, were to be thrown open to them. Even this treaty was kept a secret, but in the meantime the Confederation should send troops to the assistance of the king. But before the troops could be sent Charles was driven to take refuge with the Scots at Newcastle (May 1646), from which place he wrote forbidding Ormond "to proceed further in treaty with the rebels or to make any conditions with them."