During the later years of Elizabeth's reign the disturbed condition of the country made it impossible to convene a Parliament, and after the accession of James I. his advisers feared to summon such a body lest they might be unable to control it. Still, they never lost sight of the advantage it would be to their cause could they secure parliamentary sanction for the confiscation and plantation of Ulster, and for the new methods employed for the punishment of recusants. These for so far had behind them only the force of royal proclamations, and their legality was open to the gravest doubt. The great obstacle that must be overcome before a Parliament could be convoked was the fact that both in the House of Commons and in the House of Lords the Catholics might find themselves in a majority. To prevent such a dire catastrophe it was determined to create a number of new parliamentary boroughs so that many places "that could scarcely pass the rank of the poorest villages in the poorest country in Christendom" were allowed to return members, provided only that it was certain they would return Protestants. Nineteen of the thirty-nine new boroughs were situated in Ulster, where the plantations had given the English and Scotch settlers a preponderance. In the House of Lords the situation was also critical, but it was hoped that by summoning all the Protestant bishops and also certain peers of England who had got grants of territory in Ireland the government could count on a majority, especially as some of the Catholic lords were minors, and as such not entitled to sit. For months the plans for packing the Parliament and for preparing a scheme of anti-Catholic legislation were being concocted, and the Catholic lords, knowing well what was going on, felt so alarmed that they lodged a solemn protest with the king against the erection of towns and corporations "consisting of some few poor and beggarly cottages" into parliamentary boroughs, against the wholesale exclusion of Catholics from office on account of their religion, and conjured the king "to give order that the proceedings of Parliament may be conducted with moderation and indifferency." In spite of this protest the new boroughs were created, and the elections were carried out in the most high-handed manner, the sheriffs hesitating at nothing so long as they could secure the nomination of Protestant representatives.

On the day preceding the opening of Parliament (fixed for 18th May 1613) the Catholic Lords of the Pale addressed a protest to the Lord Deputy. They asserted that while several of the Irish Catholic nobles entitled to sit in the House of Lords were not summoned, English and Scotch lords "already parliant in other kingdoms" had been invited to attend, that new corporations had been created, many of them since Parliament was summoned, without any right or title except to assure a Protestant majority, that the sheriffs and returning officers had acted most unfairly during the election, and that a Parliament sitting "in the principal fort and castle of the kingdom," surrounded by "numbers of armed men," could not be regarded as a free assembly. When the House of Commons met on the following day the Catholics proposed that Sir John Everard, who had been dismissed from his office of judge because he refused the oath of supremacy, should be elected speaker, while the Protestants proposed Sir John Davies for this position. The Catholics, knowing well that if the returns of the sheriffs were accepted they would find themselves in the minority, maintained that the members against whose return objection had been lodged should not be allowed to vote. On this being refused, they tried to prevent a vote being taken, and when the supporters of Davies left the chamber to take a count, the Catholics installed Sir John Everard in the chair. The Protestants, claiming that they had a clear majority, one hundred and twenty-seven out of a possible two hundred and thirty-two, removed Sir John Everard by force, and adopted Sir John Davies as speaker. The Catholics then left the chamber, and both Lords and Commoners refused to attend any further sessions until they should have laid their grievances before the king. In consequence of their refusal it was necessary to suspend the parliamentary session, and both parties directed all their attention to an appeal to the king. The Catholics sent to London as their representatives, Lords Gormanston and Dunboyne, Sir James Gough and Sir Christopher Plunkett, William Talbot and Edward FitzHarris, and a general levy was made throughout the kingdom to raise money to pay their expenses. A great deal of time was wasted in inquiries in London and in Ireland. James found it difficult to decide against the Lord Deputy, while at the same time he could not shut his eyes to the justice of several of the claimants brought under his notice by the Catholics. At one time he promised their delegates that he would not interfere with the free exercise of their religion provided they admitted it was not lawful to deprive him of his crown or to offer violence to his person, but when the Lord Deputy wrote warning him of the effect this speech had produced in Ireland, James, while not denying that he had used the words attributed to him, issued a proclamation announcing that he would never grant religious toleration, and ordering all bishops, Jesuits, friars, and priests to depart from the kingdom before the 30th of September (1614). In April 1614 the king decided to annul thirteen of the returns impeached by the Catholics, but in regard to the other matters of complaint he gave judgment in favour of the Lord Deputy. In a personal interview with the Catholic lords he pointed out that it was his privilege to create as many peers and parliamentary boroughs as he liked. "The more the merrier, the fewer the better cheer." He informed them, too, that they were only half subjects so long as they acknowledged the Pope, and could, therefore, expect to have only half privileges, and expressed the hope that by their future good behaviour in Parliament they might merit not only his pardon but "his favour and cherishing."

In October 1614 Parliament was at last ready to proceed with its business. During the course of the negotiations it would appear that the plan of passing new penal legislation against Catholics was abandoned. It was intended at first to enact a very severe measure for the expulsion of Jesuits and seminary priests, and another framed with the intention of making the laws against Catholics in England binding in Ireland. But these clauses were struck out, probably as a result of a bargain between the Catholic lords and the king. In return for this toleration the Catholic lords agreed to support the Act of Attainder passed against O'Neill and O'Donnell, together with their aiders and abettors, and to approve of the wholesale confiscation that had taken place in Ulster. In vain did Florence Conry, Archbishop of Tuam, call upon the Catholic members to stand firm against such injustice. His warning, that if they consented to the robbery of their co-religionists of the North their own turn to be robbed would surely come, fell upon deaf ears. Their loyalty to England had nerved them to draw their swords against O'Neill, and it nerved them also to assist Chichester and Davies to carry on the Ulster Plantations. Well might the latter boast in his letter to the Earl of Somerset that the service performed by this Parliament was "of such importance, as greater has not been effected in any Parliament of Ireland these hundred years. For, first, the new erected boroughs have taken place, which will be perpetual seminaries of Protestant burgesses, since it is provided in the charters that the provost and twelve chief burgesses, who are to elect all the rest, must always be such as will take the Oath of Supremacy. Next, all the states of the kingdom have attainted Tyrone, the most notorious and dangerous traitor that ever was in Ireland, whereof foreign nations will take notice, because it has been given out that Tyrone had left many friends behind him, and that only the Protestants wished his utter ruin. Besides, this attainder settles the Plantation of Ulster."[31]

Chichester, who had planned the Plantation of Ulster, and who had enriched himself out of the spoils of the Northern princes, was removed from office in 1615, and was succeeded by Sir Oliver St. John, who came to Ireland determined to support the anti-Catholic campaign. In a short time more than eighty of the best citizens of Dublin were in prison because they refused the oath of supremacy, and throughout the country, jurors who refused to convict the Catholics were themselves held prisoners, so that the jails were soon full to overflowing. Immense sums were levied off both poor and rich for non- attendance at Protestant religious service. In the County Cavan, for example, the fines for one year amounted to about £8,000,[32] while large sums were paid by the Catholic noblemen for protection from the Protestant inquisitors. New plantations were undertaken, on the lines of the Ulster Plantation, in Wexford, Longford, King's County, and Leitrim, though, not having been carried out so thoroughly or so systematically as the former, they had not the same measure of success. All Catholic noblemen succeeding to property were obliged to take the oath of supremacy, though apparently they could procure exemption from this test by the payment of a fine, but the Court of Wards took care that minors should be entrusted to Protestant guardians, and should be sent if possible to Trinity College. By means such as these Elizabeth and James succeeded in Protestantising a certain number of the heirs to Irish estates. Proclamations were issued once more against the clergy, both secular and regular, and so violent was the persecution that the Bishops of Ireland addressed a petition to the Catholic rulers of Europe, and especially to the King of Spain, asking them to intercede with James on behalf of his Irish Catholic subjects (1617).[33]

The negotiations for the marriage of Prince Charles to a Spanish princess made it necessary for the king to be more guarded in his religious policy in Ireland. Oliver St. John, who had shown himself to be such a bitter enemy of the Catholics, was removed from office, and Lord Falkland was sent over as Deputy in 1622. Rumours were afloat on all sides that his policy was to be one of toleration. The Protestants were alarmed and at the installation of the new Deputy (Sept. 1622) James Ussher, then Protestant Bishop of Meath, taking as his text, "He beareth not the sword in vain," preached a violent sermon in favour of religious persecution. Primate Hampton wrote immediately to the preacher, reproving him for his imprudence, asking him to explain away what he had said about the sword, and advising him to spend more of his time in his own diocese of Meath, where matters were far from being satisfactory.[34] On the return of Charles from Spain a new proclamation was issued (1624) ordering all "titulary popish archbishops, bishops, vicars-general, abbots, priors, deans, Jesuits, friars, seminary priests, and others of that sect, made or ordained by authority derived from the See of Rome or other foreign parts to depart from the kingdom within forty days under pain of his Majesty's indignation and penalties. If any of these dared to remain, or if any persons dared to receive them, the offenders were to be lodged in prison, "to the end such further order may be taken for their punishment as by us shall be thought fit."[35]

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]