Cromwell, having taken a little time for his troops to recruit, marched on Drogheda, then held for the king by Sir Arthur Aston, and so earnestly did he push forward the siege that in a short time he carried the city by assault, and put most of the garrison and a large number of the citizens to death. Over a thousand were slaughtered in St. Peter's Church to which they had fled for refuge, and special vengeance was meted out to the clergy, none of them who were recognised being spared. Similar scenes of wholesale butchery took place at Wexford, into which his army gained admission by treachery. Ormond was unable to make headway against such a commander, and frightened at last by the prospect that opened out before him, he made overtures to O'Neill for a reconciliation. O'Neill agreed to lend his aid against Cromwell. He sent a portion of his army south, and he himself, though ill, was already on the march when he died at Cloughoughter (6 Nov. 1649). His death at such a time was an irreparable loss both to the Catholic religion and to Ireland. Had he lived, and had Ormond and his faction co-operated with him, the campaign of Cromwell might have had a very different termination. During the closing months of 1649 the situation in Ireland seemed hopeless. Though as an unscrupulous diplomatist Ormond had few equals, he was utterly worthless as a soldier, and to make matters worse he was still distrusted by the great mass of the Irish people. In the hope of restoring unity and of encouraging the people to continue the struggle a synod of the bishops and clergy assembled at Clonmacnoise (Dec. 1649). They issued a declaration warning the people that they could expect no mercy from the English Parliament, that the wholesale extirpation of Catholicism was intended, as was evidenced by the actions of Cromwell, and that the lands of the Irish Catholics were to be handed over to English adventurers. They called upon them to forget past differences, to sink racial and personal jealousies, and to unite against the common enemy. But the country distrusted Ormond, and refused to rally to his standard. Another meeting consisting of the bishops and of the Commissioners of Trust was held at Loughrea, in which it was agreed that there should be a general levy of all men fit to bear arms, and the monastery of Kilbegan was fixed as the place of rendezvous. Several of the cities and leading men refused, however, to take any part in a movement controlled by Ormond, and as a last desperate resort, at the meeting of the bishops held at Jamestown (12 Aug. 1650) the bishops declared that there could be no hope of unity unless Ormond surrendered his trust to some person in whom the entire country had confidence. Very reluctantly Ormond agreed to this request and left Ireland in December, having appointed the Earl of Clanrickard as his successor. The latter was a Catholic who had played a very ignoble part throughout the war. Had he displayed years before but half the energy he displayed in its later stages things might never have come to such a pass.
As it was, Cromwell made great progress in the South, though he was forced to raise the siege of Waterford, and suffered a bad defeat at Clonmel from the nephew of O'Neill. He left Ireland in May 1650, and entrusted the command to Ireton. Owing to the state of disunion Ireton was enabled to take city after city. Limerick was taken in 1651, and Terence O'Brien, Bishop of Emly, was put to death. Bishop MacMahon of Clogher, who had assumed the leadership of the army of Owen Row O'Neill after the latter's death was defeated at Scarrifhollis (1650). Later on he was captured, and put to death, his head being impaled on the gates of Enniskillen as a warning to his co-religionists. The submission of Clanrickard in 1652 practically put an end to the war, and before another year had elapsed all effective resistance had ceased.
During the Kilkenny Confederation the Catholic Church was restored to its original position. In the districts controlled by the Confederates the bishops and clergy were allowed to occupy once more their houses and churches wherever these had not been destroyed, and religious communities of both men and women were set up again close to their former monasteries and convents, though at the same time the Catholic Lords of the Pale were alert lest they should be asked to return any of the ecclesiastical or monastic lands that had been granted to them by royal patent. In Dublin and wherever Ormond and the Royalists had authority, both clergy and people enjoyed complete toleration, but in certain portions of the North, and wherever the Puritans and Parliamentarians held sway, persecution was still the order of the day. When Dublin was surrendered to the Parliamentarians (1647) the priests, and later on, all Catholics, were expelled from the city. In the South of Ireland Lord Inchiquin acted in the most savage manner in Cashel and generally in the cities which he conquered, while the Parliamentarian party in the North showed no mercy to the Catholics who fell into their hands. After the arrival of Cromwell the prospect became even more gloomy. Though he announced that he would interfere with no man's religion, he declared that on no account could he tolerate the celebration of Mass. The clergy were put to the sword in Drogheda and Wexford. The Archbishop of Tuam was killed during the war (1645); Boetius Egan, Bishop of Ross, fell into the hands of Lord Broghill and was put to a cruel death because, instead of advising the garrison of Carrigdrohid to surrender, he encouraged them to continue the struggle (1650); Terence Albert O'Brien, Bishop of Emly, was captured by Ireton after the siege of Limerick, and was hanged; Heber MacMahon, Bishop of Clogher, was put to death by the orders of Coote (1650); Bishop Rothe of Ossory died as a result of the sufferings he endured, and Bishop French of Ferns, after undergoing terrible trials in Ireland, was obliged to make his escape to the Continent.
In arranging the terms of surrender the Cromwellian generals sometimes excluded the bishops and clergy from protection, and at best they granted them only a short time to prepare for leaving the country. The presence of the priests was regarded as a danger for the projected settlement of Ireland, and hence the order was given (1650) that they should be arrested. In 1650 a reward of ￡20 was offered to any one who would betray the hiding place of any Jesuits, priests, friars, monks, or nuns. At first those clergy who were captured were sent into France and Spain, but later on large numbers of them were shipped to the Barbadoes. Thus, for example, in 1655 an instruction was sent to Sir Charles Coote that the priests and friars then captive in Galway who were over forty years of age should be banished to Portugal or France, while those under that age were to "be shipped away for the Barbadoes or other American plantations." For those who returned death was the penalty that was laid down. Since the priests still contrived to elude their pursuers by disguising themselves as labourers, peasants, beggars, gardeners, etc., an order was issued in 1655 that a general search should be made throughout Ireland for the capture of all priests. Five pounds was to be paid to any one who would arrest a priest, and more might be awarded if the individual taken were of special importance. When the jails were well filled, another instruction was issued that the priests should be brought together at Carrickfergus for transportation. Here it was claimed that some offered to submit to the terms of the government rather than allow themselves to be sent away, but as the statement comes from an unreliable source it should be received with caution. In 1657 Major Morgan, representative of Wicklow in the United Parliament of England and Ireland, declared: "We have three beasts to destroy that lay heavy burthens upon us. The first is the wolf, on whom we lay five pounds a head of a dog, and ten pounds if a bitch. The second beast is a priest, on whose head we lay ten pounds, and if he be eminent, more. The third beast is a Tory, on whose head, if he be a public Tory we lay twenty pounds, and forty shillings on a private Tory." Towards the end of the Protectorate the government, instead of transporting the priests abroad, sent them in crowds to the Island of Aran and to Innisbofin. "The Lord Deputy and Council," wrote Colonel Thomas Herbert (1658), "did in July last give order for payment of ￡100 upon account to Colonel Sadleir, to be issued as he should conceive fit for maintenance of such Popish priests as are or should be confined to the Isle of Boffin, according to six-pence daily allowing, building cabins and the like. It is not doubted but care was taken accordingly, and for that the judges in their respective circuits may probably find cause for sending much more priests to that island, I am commanded to signify thus much unto you that you may not be wanting to take such care in this business as according to former directions and provision is made."鈥淏鈥檛
Already in 1642 the English Parliament had passed measures for the wholesale confiscation of Catholic Ireland, and had pledged the land to these "adventurers" who subscribed money to carry on the war. In 1652, when the reduction of Ireland was practically complete, it was deemed prudent to undertake the work of clearing Leinster and Munster of its old owners to prepare the way for the adventurers and for the soldiers, whose arrears were paid by grants of farms or estates. According to the terms of the Act and of the Instructions issued in connexion with it all Irish Catholics were commanded to transplant themselves to Connaught before the 1st May 1654 under pain of being put to death by court-martial if they were found after that date east of the Shannon. Exceptions were indeed made in the case of those women who were married to English Protestants before December 1650, provided that they themselves had become Protestant; in case of boys under fourteen and girls under twelve in Protestant service and who would be brought up Protestants, and lastly in case of those who could prove that for the previous ten years they had maintained "a constant good affection" towards the Parliament. The order to transplant was notified throughout Ireland, and a commission was set up at Loughrea to consider claims and to make assignments of land in Connaught, all of which was to be at the disposal of the Irish except a prescribed territory along the sea-board. Even the inhabitants of Galway, who had submitted only on the express condition of retaining their lands, were driven out of the city, and the city itself was handed over to the corporations of Gloucester and Liverpool to recoup them for the losses they had suffered during the Civil War. Petitions began to pour in for mercy or at least for an extension to the time-limit, but though on the latter point some concessions were made, few individuals were allowed any reprieve. The landowners were marked men, and they were obliged to go. It would be impossible to describe the hardship and miseries suffered by those who were forced to leave their own homes, and to seek a refuge in what was to them a strange country. To ease the situation large numbers of the men capable of bearing arms were shipped to Spain, or to others of the Continental countries, but soon it was thought that this was bad policy likely only to serve some of England's rivals. It was then determined to transport large numbers to the West Indies, the Barbadoes, Jamaica, and the Caribee Islands. Ship-loads of boys and girls were seized according to orders from England, and were sent out of the country under the most awful conditions to a land where a fate awaited many of them that was worse than death. The magistrates had no scruple in committing all Catholics who remained east of the Shannon and who were brought before them, as vagrants, and then they were hurried off to the coast.鈥淏鈥檛
At first the idea was to remove the native population entirely from Leinster and Munster lest the soldiers and "adventurers" might be contaminated, and stern measures were taken to prevent any of the officers or men from taking Irish wives. Ireton laid it down that any officer or soldier who dared to marry an Irish girl until she had been examined by a competent board to see whether her conversion flowed "from a real work of God upon her heart," should be punished severely. But later on petitions poured in from the new Protestant landowners to be allowed to keep Catholics as servants and labourers, and on the understanding that the masters would utilise this opportunity to spread the true religion, their requests were granted. Some obtained dispensations or at least managed to secure delays; others probably were able to come to terms with the soldiers to whom their farms had fallen in the general lottery, and others still preferred to risk the danger of transportation by remaining in their own district rather than to seek a new home. Had the Protectorate lasted long enough the policy of transplanting might have succeeded, but as it was the Cromwellian planters soon disappeared or became merged into the native population, and in spite of all the bloodshed and robbery, the people of Ireland generally were as devoted to the Catholic religion in 1659 as they had been ten years before.鈥淏鈥檛
When it became clear from the course of events in England that Charles II. was about to be restored to the throne Lord Broghill and Sir Charles Coote, both of whom had helped to crush the Irish Royalists and had profited largely by the Revolution, hastened to show their zeal for the king's cause. The Catholics who had fought so loyally for his father hoped that at last justice would be done to them by re-instating them in the lands from which they had been driven by the enemies of the king. But Charles was determined to take no risks. He sent over the Duke of Ormond, the most dangerous enemy of the Catholic religion in Ireland, as Lord Lieutenant (1660). A Parliament was called in 1661, and as the Catholics had been driven from the corporate towns during the Cromwellian régime and as the Cromwellian planters were still in possession, the House of Commons was to all intents and purposes Protestant. An Act of Settlement was passed whereby Catholics who could prove their "innocence" of the rebellion were to be restored, but the definition of innocence in the case was so complicated that it was hoped few Catholics, if any, would succeed in establishing their claims (1661). A Court of Claims composed of five Protestant Commissioners, was set up to examine the individual cases, but in a short time, when it was discovered that a large number of Catholics were succeeding in satisfying the conditions laid down by law for restoration to their property, an outcry was raised by the planters, and the Court of Claims was suspended (1664). The Act of Explanation was then passed to simplify the proceedings, as a result of which act two-thirds of the land of Ireland was left in the hands of the Protestant settlers. Close on sixty of the Catholic nobility were restored as a special favour by the king, but a large body of those who had been driven out by Cromwell were left without any compensation.鈥淏鈥檛
In consequence of the Cromwellian persecution nearly all the bishops and a large body of the clergy, both secular and regular, had been driven from Ireland, but after the accession of Charles, who was known to be personally friendly to the Catholics, many of them began to return. It would be a mistake, however, to imagine that the persecution had ceased, or that the laws against the clergy were not put in force in several districts. Ormond returned to Ireland as hostile to Catholicity as he had been before he was driven into exile; and as he thought that he had a particular grievance against the Irish bishops he was determined to stir up the clergy against them, to divide the Catholics into warring factions, and by favouring one side to create a royalist Catholic party as distinct from the ultramontane or papal party. For this work he had at hand a useful instrument in the person of Father Peter Walsh, a Franciscan friar, who had distinguished himself as a bitter opponent of the nuncio and as a leader of the Ormondist faction in the Supreme Council. In 1661 it was determined by some leading members, both lay and clerical, to present an address of welcome to Charles II., but by the influence of Walsh and others the address, instead of being a mere protestation of loyalty, was framed on the model of the Oath of Allegiance (1605), which had been condemned more than once by the Pope. Many of the Catholic lords indicated their agreement with this address or Remonstrance, as it was called, and some of the clergy, deceived by the counsels of Father Walsh, expressed their willingness to adhere to its terms. Ormond, who spent money freely in subsidising Walsh and his supporters, had good reason to be delighted with the success of his schemes. Grave disputes broke out among the clergy, which the government took care to foment by patronising the Remonstrants and by wreaking its vengeance on the anti-Remonstrants on the grounds of their alleged disloyalty. To bring matters to a crisis it was arranged by Walsh and Ormond that a meeting of the bishops, vicars, and heads of religious orders should be held in Dublin (June 1666). In addition to Dr. O'Reilly, Archbishop of Armagh, Bishops Plunkett of Ardagh, and Lynch of Kilfenora, there were present a number of vicars of vacant dioceses together with representatives of the Franciscans, Dominicans, Augustinians, Capuchins, and Jesuits. Dr. O'Reilly spoke strongly against the terms of the Remonstrance as being highly disrespectful to the Pope, and the majority of those present supported his contention. They expressed their willingness to present an address of loyalty from which the objectionable clauses should be omitted. But Walsh, dissatisfied with anything but a complete submission, shifted the ground of the debate, by endeavouring to secure the acceptance of the assembly of the pro-Gallican declaration of the Sorbonne (1663). Even still his efforts were far from being successful, and the meeting was dissolved by Ormond. The primate was kept a prisoner in Dublin for some months, and then transported to the Continent, while the other members present were obliged to make their escape from Ireland or to go into hiding. By orders of Ormond close watch was kept upon the clergy who sided against the Remonstrance, and many of them were thrown into prison.鈥淏鈥檛