A full account of the position of the Catholics of Ireland is given in a letter written from Dublin in 1623. Catholic minors were compelled to accept the oath of supremacy before they could get letters of freedom from the Court of Wards (established 1617); all mayors, magistrates, officials, etc., of corporate towns were commanded to take the oath under penalty of having their towns disenfranchised; priests were arrested and kept in prison; laymen were punished by sentences of excommunication and by fines for non-attendance at Protestant worship; they were summoned before the consistorial courts for having had their children baptised by the priests and were punished with the greatest indignities; Catholics were forbidden to teach school and Catholic parents were forbidden to send their children abroad; the Catholic inhabitants of Drogheda were indicted before a Protestant jury, and having been found guilty of recusancy, they stood in danger of having all their property forfeited; in Louth the juries were ordered to draw up a list of Recusants; when three Catholic jurors refused they were thrown into prison and obliged to give security to appear before the Dublin Star Chamber; and in Cavan proceedings of a similar kind were taken.[36]

Amongst the distinguished bishops of the Irish Church at this period were Peter Lombard, Archbishop of Armagh (1601-25), a native of Waterford, who studied at Oxford and Louvain, was appointed a professor at the latter seat of learning, took a very prominent part in the /Congregatio de Auxiliis/, published some theological treatises together with an ecclesiastical history of Ireland, entitled, /De Regno Hiberniae, Sanctorum insula, Commentarius/,[37] but who on account of the danger of stirring up still greater persecution never visited his diocese; Eugene Matthews or MacMahon, Bishop of Clogher (1609) and Archbishop of Dublin (1611) who did splendid work for the Irish Church by the decrees passed in the provincial synod at Kilkenny (1614) as well as by his successful efforts for the foundation of the Pastoral College at Louvain; David O'Kearney, appointed to Cashel (1603) as successor to the martyred Archbishop O'Hurley, who though hunted from place to place continued to fill the duties of his office till about the year 1618, when he went to Rome; and Florence Conry, Archbishop of Tuam, a Franciscan, who served with the army of the Northern Princes, and who was specially detested by the English government on account of his loyal defence of O'Neill. Not being allowed to return to Ireland, he devoted himself to the study of theology, and was the author of several very important works, some of which were not, however, free from the suspicion of something akin to Jansenism. By far the most useful book he composed was his celebrated Irish Catechism published at Louvain in 1626.[38]

During the opening years of the reign of Charles I. (1625-49) the persecution was much less violent, and as Charles was married to a French Catholic princess and as he had promised solemnly not to enforce the laws against Catholics, it was hoped that at long last they might expect toleration. The distinguished Franciscan Thomas Fleming, son of the Baron of Slane, who had received his education in the Irish Franciscan College at Louvain, was appointed Archbishop of Dublin (1623), and arrived in Ireland two years later. He was able to report that the conduct of the Catholics not only in Dublin but throughout Ireland was worthy of every praise, and to point to the fact that many who made the pilgrimage to St. Patrick's Purgatory in Lough Derg were obliged to return without satisfying their pious desires because the island was so crowded that there was no room for them to land. Chapels were opened in some of the less pretentious streets in Dublin; communities of religious orders took up fixed residences in the capital; and the Jesuits summoned home some of their ablest teachers to man a Catholic University which they opened in Back Lane (1627). The government stood in need of money to equip and support a new army, then considered necessary on account of the threatening attitude of France, and in order to obtain funds a large body both of the Protestant and Catholic nobility were invited to come to Dublin for discussion. They were offered certain concessions or "Graces" in return for a subsidy, and to placate the Catholic peers it was said that the fines for non-attendance at church would not be levied, and that they might expect tacit toleration.

The very mention of toleration filled the Protestant bishops with alarm, and, considering the fact that they were dependent upon coercion for whatever congregations they had, their rage is not unintelligible. James Ussher, who had become Protestant Primate of Armagh, convoked an assembly of the bishops. They declared that: "The religion of the Papists is superstitious and idolatrous, their church in respect of both, apostatical. To give them, therefore, a toleration, or to consent that they may freely exercise their religion, and profess their faith and doctrine is a grievous sin, and that in two respects. For it is to make ourselves accessory, not only to their superstitions, idolatries, and heresies, and in a word, to all the abominations of Popery; but also, which is a consequent of the former, to the perdition of the seduced people, which perish in the deluge of Catholic apostacy. To grant them toleration, in respect of any money to be given, or contribution to be made by them, is to set religion to sale, and with it, the souls of the people, whom Christ our Saviour hath redeemed with His most precious blood."[39] The Irish deputies arrived in London to seek a confirmation of the "Graces" at the very time that the third Parliament of Charles (1627) was petitioning him to put in force the laws against the Recusants. The members of the English House of Commons complained that religious communities of men and women had been set up in Dublin and in several of the larger cities, that Ireland was swarming with Jesuits, friars, and priests, that the people who attended formerly the Protestant service had ceased to attend, that in Dublin there were thirteen mass- houses, and that Papists were allowed to act as army officers, and Papists were being trained as soldiers."[40] In these circumstances the Catholic members of the deputation consented to abandon their claims for full toleration, though it was understood that the fines levied on account of absence from Protestant service would not be enforced, but they were promised that Catholic lawyers would be allowed to practise without being obliged to take the oath of supremacy. In return for the promised "Graces," which were to be ratified immediately in Parliament, the Irish nobles promised to pay a sum of ￡120,000 for the support of the new army.

The promised Parliament was not held, nor were the "Graces" conceded either to the Irish generally or to the Catholics. Still, there was no active persecution for some time. The provincial of the Carmelites in Dublin was able to report to the Propaganda (1629) that "all the ecclesiastics now publicly perform their sacred functions, and prepare suitable places for offering the holy sacrifice, and that with open doors; they now preach to the people, say Mass, and discharge all their other duties without being molested by any one." The Carmelites, he wrote, "had a large church, but not sufficient to contain one-sixth of the congregation; the people flocked in crowds to Confession, and Holy Communion; the Franciscans, Dominicans, Capuchins, and Jesuits were hard at work; and the parishes were supplied with parish priests who resided in their districts and were supported by the voluntary offerings of the people."[41] From a report of the year 1627, it is clear that the Dominicans had over fifty priests of their Order in Ireland, together with several novices and students.[42]

But already the enemies of the Catholic religion were at work, and, as a result, a proclamation was issued by Lord Falkland in 1629 commanding that all monasteries, convents, colleges, and religious houses should be dissolved, that all religious and priests should cease to teach or to perform any religious service in any public chapel or oratory, or to teach in any place whatsoever in the kingdom, and that all owners of religious houses and schools should apply them to other uses without delay (1629). At first no notice was taken of this proclamation in Dublin or in any of the cities of Ireland. Ussher wrote to complain of the "unreverend manner" in which the proclamation was made in Drogheda. "It was done in scornful and contemptuous sort, a drunken soldier being first set up to read it, and then a drunken sergeant of the town, making the same to seem like a May-game." The priests and friars merely closed the front doors of the churches, he said, but the people flocked to the churches as usual by private passages.[43] Lord Falkland does not seem to have made any determined effort to carry out the royal proclamation in Dublin, but unfortunately he was recalled in 1629, and in the interval from his departure till the arrival of Sir Thomas Wentworth (1632) Loftus, Viscount of Ely, and Lord Cork were appointed as Lords Justices. Immediately the persecution began. The Protestant Archbishop of Dublin, accompanied by a body of soldiers, made a raid upon the Carmelite Church in Cook Street while Mass was being celebrated on St. Stephen's Day, destroyed the altar and statues, and seized two of the priests; but the people set upon the archbishop and the soldiers, and rescued the prisoners. The troops were called out at once, and several of the Dublin aldermen were lodged in prison. Most of the churches were seized, and the Jesuit University was given over to Trinity College. Attacks of a similar kind were made on the houses and churches of the regular clergy in Cork, Waterford, Limerick, and in various other parts of the country. An order was issued by the Lords Justices that St. Patrick's Purgatory together "with St. Patrick's bed and all the vaults, cells, and all other houses and buildings should be demolished, and that the superstitious stones and material should be cast into the lough." Catholic deputies hastened to London to lay their grievances before the king, but, though he was not unwilling to help them, he found it difficult to do much for them on account of the strong anti-Catholic feeling in England. Queen Henrietta Maria did appeal to the new Deputy to restore St. Patrick's Purgatory, but, as it was situated "in the midst of the great Scottish Plantation," he feared to grant her request at the time. Lord Cork reported that "he had set up two houses of correction in dissolved friaries, in which the beggarly youths are taught trades." But soon the king and Wentworth grew alarmed about the storm that the justices were creating in Ireland. The Catholic lords threatened that unless an end were put to the persecution, which was contrary to the "Graces" that had been promised, they would refuse to pay the subsidy they had promised, and letters were sent both by the king and Wentworth throwing the blame on Loftus and Lord Cork, and reproving them for what they had done.[44]

In 1632 Sir Thomas Wentworth, afterwards Earl of Strafford, arrived in Ireland as Lord Deputy. He was a strong man, intensely devoted to the king, and determined to reduce all parties in Ireland to subjection. In religion he was a High Churchman of the school of Laud, and opposed to the Scotch Presbyterians of the North of Island almost as much as to the Irish Catholics. From the beginning he was determined to raise the revenues of the crown in Ireland, to establish a strong standing army, and to secure the future peace of the country by carrying out a scheme of plantations in Connaught and Munster along the lines followed by the advisers of James I. in case of Ulster. One of his first acts after his arrival in Ireland was to commission Dr. John Bramhall, afterwards Protestant Bishop of Derry and Primate, to hold an inquiry into the state of the Protestant Church. The latter, after having made some investigations, informed Archbishop Laud that he found it difficult to say "whether the churches were more ruinous and sordid or the people irreverent in Dublin," that one parochial church in Dublin had been converted into a stable, another had become a nobleman's mansion, while a third was being used as a tennis-court, of which the vicar acted as keeper. The vaults of Christ's Church had been leased to Papists "as tippling rooms for beer, wine, and tobacco," so that the congregation stood in danger of being poisoned by the fumes, and the table for the administration of Holy Communion was made "an ordinary seat for maids and apprentices." "The inferior sorts of ministers were below all degrees of contempt, in respect of their poverty and their ignorance," and it was told him that one bishop held three and twenty benefices with care of souls.[45]

Wentworth lost no time in trying to raise money for the army, but many of the lords, both Catholic and Protestant, were so annoyed at the refusal to confirm the "Graces" and at the delay in calling the Parliament that had been promised, that Wentworth was forced to make some concession. Parliament was convoked to meet in 1634, and the Lord Deputy nominated his own supporters in the boroughs, so as to counter- balance the representation from the counties, which representation he could not in all cases control. The Catholics were strong in the Lower House particularly, but care was taken that they should be in a minority. The main question was the granting of subsidies, but several of the Protestants and all the Catholics demanded that the "Graces" should first be confirmed. Both Protestant and Catholic landowners were interested in safeguarding the titles to their property by having it enacted that sixty years' possession should be regarded as a sufficient proof of ownership. As such an enactment would have upset all Wentworth's plans for a wholesale plantation, he succeeded in resisting such a measure, and partly by threats, partly by underhand dealings with particular individuals he obtained a grant of generous subsidies without any confirmation of the "Graces." In April 1635 Parliament was dissolved, and almost immediately the Lord Deputy made preparations for acting under the commission for inquiring into defective titles granted to him by the king. "All the Protestants are for plantations," he wrote, "and all the others are against them. If the Catholic juries refuse to find a verdict in favour of the king, then recourse must be had to Parliament, where a Protestant majority is assured." Portions of Tipperary, Clare, and Kilkenny were secured without much difficulty, but nothing less than the whole of Connaught would satisfy the Deputy. Roscommon was the first county selected, and the Commissioners, including the Lord Deputy, arrived in Boyle to hold the inquiry (July 1635). The jury, having been informed by Wentworth that, whether they found in his favour or not, the king was determined to assert his claims to their county, and that their only hope of mercy was their prompt obedience, delivered the required verdict. Sligo and Mayo also made their submission. In Galway, however, the jury found against the king. In consequence of this the sheriff was fined ￡1,000 and placed under bail to appear before the Star Chamber, and the jurymen were threatened with severe punishment. They were fined ￡4,000 each and ordered to be imprisoned till they should pay the full amount. In this way the whole of Connaught, with the exception of Leitrim which was planted already, together with a great part of Clare, Tipperary, and Kilkenny was confiscated to the crown. But Wentworth postponed the plantation of Connaught to a more favourable period, and before any such period arrived he had lost both his office and his head. The danger to Charles I. from the Scotch Covenanters was already apparent, and Charles urged his Deputy to raise an army in Ireland. During the years 1639 and 1640 the work of training the army, many of the officers of which and most of the soldiers, were Catholics, was pushed forward, but the triumph of the Scots and the execution of the Earl of Strafford in April 1641 made it impossible to use it for the purpose for which it was designed. Acting on the instigation of the English Parliament, Charles sent an order that the Irish troops should be disbanded, and added that he had licensed certain officers to transport eight thousand troops to the aid of any of the sovereigns of Europe friendly to England. For one reason or another very few of the soldiers left Ireland, as both their own leaders and the king knew well that their services would be soon required at home. Parliament had met in Ireland in March 1640,[46] and, having voted several subsidies to aid the king, it adjourned. When it met again in 1641 the Catholics were actually in the majority, and seemed determined to hold their own. The king wrote to confirm the "Graces," and to suggest that a bill should be introduced to confirm defective titles in Tipperary, Clare, and Connaught, but the obstructive tactics of the Earl of Ormond, and the unfavourable attitude of the Lords Justices, Sir William Parsons and Sir William Borlase, towards Catholic claims, prevented anything being done. Parliament was adjourned till the 9th November, but before that date arrived the issues had been transferred to another and a different court.[47]