The appeal of these Catholic lords, backed[8] as it was by the danger of a new and more general rebellion, was not without its effects in England. In January 1607 the privy council in England wrote to Sir Arthur Chichester, Lord Deputy, that although "the reformation of the people of Ireland, extremely addicted to Popish superstition by the instigation of the seminary priests and Jesuits, is greatly to be wished and by all means endeavoured, still, a temperate course ought to be preserved." There should be no question of granting toleration, but at the same time there should be no "startling of the multitude by any general or rigorous compulsion." The principal men in the cities who show themselves to be the greatest offenders should be punished; the priests and friars should be banished, but no "curious or particular search" should be made for them; Viscount Gormanston and his companions should be released under recognisances, except Sir Patrick Barnewall who was to be sent into England; the Dublin aldermen should be treated in a similar manner but should be obliged to pay the fines, and the Protestant clergy should be exhorted to take special pains to plant the new religion "where the people have been least civil."[9]

But Chichester, Davies, Brouncker, and their companions had no intention of listening to the counsels of moderation. They continued to indict the poorer classes according to the clauses of the Act of Uniformity and to cite the wealthier citizens before the Star Chamber for disobedience to the royal mandates.[10] In Waterford Sir John Davies reported "we proceeded against the principal aldermen by way of censure at the council table of the province for their several contempts against the king's proclamations and the special commandments of the Lord President under the council seal of Munster. Against the multitude we proceeded by way of indictment upon the Statute of 2 Elizabeth, which giveth only twelve pence for absence from church every Sunday and holiday. The fines imposed at the table were not heavy, being upon some £50 apiece, upon others £40, so that the total sum came but to £400; but there were so many of the commoners indicted that the penalty given by the statute (twelve pence) came to £240 or thereabouts."[11] Punishments of a similar kind were inflicted in New Ross, Wexford, Clonmel, Cashel, Youghal, Limerick, Cork, and in all the smaller towns throughout Munster. In Cork the mayor was fined £100, and in Limerick more than two hundred of the burgesses were indicted, the fines paid by these being given for the repair of the cathedral.[12] Steps were also taken in Connaught to enforce attendance at the Protestant service. Five of the principal citizens of Galway were summoned before the court and fined in sums varying from £40 to £20, and punishments of a lesser kind were inflicted in other portions of the province. In Drogheda "the greatest number of the householders together with their wives, children, and servants," were summoned and fined for non-attendance at church. In Meath, Westmeath, Longford, King's County, and Queen's County the government officials were particularly busy.

But though here and there a few of the prominent citizens and of the poorer classes were driven into public conformity by fear of punishment, the work of winning over the people to Protestantism made little progress. In Cashel the Commissioners reported (1606) that they found only one inhabitant who came to church, and even "the Archbishop's (Magrath) own sons and sons-in-law dwelling there" were noted as obstinate recusants."[13] Brouncker, President of Munster, was particularly severe in his repressive measures, so much so that on his death (1606) his successors were able to announce "that almost all the men of the towns are either prisoners or upon bonds and other contempts," but they added the further information that many of those who had been conformable in his time had again relapsed. The Protestant Bishop of Cork complained (1607) that in Cork, Kinsale, Youghal, and in all the country over which he had charge no marriages, christenings, etc., were done except by Popish priests for seven years, that the country was over-run by friars and priests who are called Fathers, that every gentleman and lord of the country had his chaplains, that "massing is in every place, idolatry is publicly maintained, God's word and his truth is trodden down under foot, despised, railed at, and contemned of all, the ministers not esteemed —no not with them that should reverence and countenance them." "The professors of the gospel," he added, "may learn of these idolators to regard their pastors."[14] Sir John Davies with his usual keen insight placed the blame for the comparative failure of the Protestant clergy. "If our bishops, and others that have care of souls," he wrote (1606), "were but half as diligent in their several charges as these men [the Jesuits and seminary priests] are in the places where they haunt, the people would not receive and nourish them as now they do. But it is the extreme negligence and remissness of our clergy here which was first the cause of the general desertion and apostasy, and is now again the impediment of reformation."[15] The Catholics had protested continually against the proceedings under royal mandates as illegal, and their protests were brought before the English privy council by Sir Patrick Barnewall, who had been sent over to London as a prisoner. The judges in England condemned the proceedings in Ireland as unwarrantable and without precedent. Barnewall was allowed to return to Ireland in 1607, and the new method of beggaring or Protestantising the wealthier class of Irish Catholics was dropped for the time.

The king had been advised, too, to enforce the oath of supremacy in case of all officials of the crown. Though in the beginning of the reign of Elizabeth something had been done in that direction, yet, in later times, owing to the dangerous condition of the country Catholic officials were not called upon to renounce the Pope. As a result, when James ascended the throne many of the judges were Catholic, as were, also, the great body of the lawyers. In response to the advice from Ireland that judges who refused to attend church and to take the oath should be dismissed, and that "recusant" lawyers should be debarred from practising in the courts, James instructed the council to induce John Everard, a Justice of the Common Pleas, to resign or conform. The mayors and aldermen of the cities, too, had never taken the oath of supremacy. In 1607 the Lord Deputy and council of Ireland informed the privy council in England that, "most of the mayors and principal officers of cities and corporate towns, and justices of the peace of this country birth refuse to take the oath of supremacy, as is requisite by the statute, and for an instance, the party that should this year have been Mayor of Dublin, avoided it to his very great charges, only because he would not take the oath." The contention apparently was that the mayors not being crown officials were not bound to take the oath, but the lawyers decided against such a view, and steps were taken to imprison those mayors who refused, and to destroy the charts of recusant corporations. Still in spite of the attempted banishment of the clergy, the enforcement of attendance at church by fines, and the punishment inflicted on the officials who refused to take the oath, the Deputy and council were forced to admit that they had made no progress. "The people," they wrote (1607), "in many places resort to Mass now in greater multitudes, both in town and country, than for many years past; and if it chance that any priest known to be factious and working be apprehended, both men and women will not stick to rescue the party. In no less multitudes do these priests hold general councils and conventicles together many times about their affairs; and, to be short, they have so far withdrawn the people from all reverence and fear of the laws and loyalty towards his Majesty, and brought their business already to this pass, that such as are conformed and go to church are everywhere derided, scorned, and oppressed by the multitude, to their great discouragement, and to the scandal of all good men."[16]

Although the persecution of James I. was violent the Catholics were well prepared to meet the storm. The Jesuits had sent some of their best men to Ireland, including Henry Fitzsimon, who was thrown into prison, and after a long detention sent into exile, Christopher Holywood, James Archer, Andrew Morony, Barnabas Kearney, etc., and, although there were complaints that their college in Salamanca showed undue favour to the Anglo-Irish, this college as well as the other colleges abroad continued to pour priests into Ireland both able and willing to sustain the Catholic religion. The Dominicans and Franciscans received great help from their colleges on the Continent so that their numbers increased rapidly, and they were able to devote more attention to instructing the people. As in England, the young generation of priests both secular and regular, sent out from the colleges in France, Spain, and the Netherlands were much more active and more determined to hold their own than those who had preceded them. They were in close touch with Rome where their agents kept the Papal Court informed of what was going on in Ireland. Clement VIII. hastened to send his congratulations to James I. on his accession to the throne, and to plead with him for toleration for his Catholic subjects. James White, Vicar-general of Waterford, wrote (1605) to inform Cardinal Baronius of the measures that had been taken to suppress the Catholic religion and to offer his good wishes to Paul V. The latter forwarded a very touching letter in which he expressed his sympathy with the Irish Church, commended the fidelity of the Irish people, and exhorted them to stand firm in the face of persecution.[17] The only weak point that might be noted at this period was the almost complete destruction of the Irish hierarchy. O'Devany of Down and Connor, Brady the Franciscan Bishop of Kilmore, and O'Boyle of Raphoe were the only bishops remaining in the province of Ulster since the murder of Redmond O'Gallagher of Derry. Peter Lombard had been appointed Archbishop of Armagh (1601), but he never visited his diocese. In the province of Leinster Matthew de Oviedo, a Spanish Franciscan, had been appointed to Dublin (1600), and had come to Kinsale with the forces of Spain. He returned to plead for a new expedition to Ireland. Another Spanish Franciscan, Francis de Ribera, had been appointed to Leighlin (1587), but he died in 1604 without having done any work in his diocese. The rest of the Sees in Leinster were vacant. In Munster, David O'Kearney was named Archbishop of Cashel (1603), and soon showed himself to be a man of great activity and fearlessness. Dermod McCragh of Cork had been for years the only bishop in the province, and had exercised the functions of his office not merely in the South, but throughout the province of Leinster. In the province of Tuam all the Sees were vacant. Wherever there was no bishop in residence care was taken to appoint vicars. In Dublin Bernard Moriarty who acted as vicar was arrested in the Franciscan convent at Multifernan in 1601, and died in prison from the wounds he received from the soldiers. Robert Lalor who acted in the same capacity was arrested, tried, and banished in 1606.[18]

Although the Earl of Tyrone had been restored to his estates and had been received graciously by the king (1603), he was both distrusted and feared by the government. Sir Arthur Chichester, who had come to act as Lord Mountjoy's deputy in 1605, and who was appointed Lord Lieutenant on the death of the latter (1607), was determined to get possession of Ulster either by driving O'Neill into rebellion or by bringing against him some charge of conspiracy. New and insulting demands were made upon O'Neill; the Protestant Archbishop of Armagh and the Protestant Bishop of Derry and Raphoe claimed large portions of his territories as belonging to their churches, and some of the minor chieftains were urged on to appeal against him to the English authorities. Having learned in 1607 that he stood in danger of arrest, he and Rory O'Donnell determined to leave Ireland. In September 1607 they sailed from Rathmullen, and on the 4th October they landed in France. After many wanderings they made their way to Rome, where they received a generous welcome from Paul V. O'Donnell died in 1608, and O'Neill, who had cherished till the last a hope of returning to Ireland, died in 1616.[19] Both chieftains were laid to rest in the Church of St. Pietro di Montorio. Although the flight of the Earls caused a great sensation both in England and Ireland, and although James I. was said to have been pained by their departure and even to have thought for a time of granting religious toleration, Chichester and his companions were delighted at the result of their work. The flight of Tyrone and Tyrconnell, the attempted rebellion of Sir Cahir O'Doherty, and the trumped-up charges brought against some of the other noblemen in the North opened up the prospect of a new and greater plantation than had ever been attempted before. Tyrone, Fermanagh, Donegal, Derry, Armagh, and Cavan were confiscated to the crown at one stroke, and preparations were made to carry out the plantation in a scientific manner. The greater portion of the territory was divided into lots of two thousand, one thousand five hundred, and one thousand acres. The Undertakers who were to get the largest grants were to be English or Scotch Protestants and were to have none but English or Scotch Protestant tenants, those who were to get the one thousand five hundred acres were to be Protestants themselves and were to have none but Protestant tenants, while the portions of one thousand acres each might be parcelled out amongst English, Scotch, or Irish, and from these Catholics were not excluded. Thousands of acres were appropriated for the support of the Protestant religion, for the maintenance of Protestant schools, and for the upkeep of Trinity College. A small portion was kept for a few of the old Catholic proprietors, and the remainder of the population were ordered to leave these districts before the 1st May 1609. Many of them remained, however, preferring to take small tracts of the mountain and bog land from the new proprietors than to trust themselves among strangers; but a great number of the able-bodied amongst them were caught and shipped to serve as soldiers in the army of Sweden.[20]

For some time after the flight of the Earls there seems to have been a slight lull in the persecution, the king and his advisers fearing perhaps that their action was only a prelude to a more general rebellion in the course of which O'Neill might return at the head of a Spanish force. But once it was clear that no danger was to be apprehended the Irish officials began to urge once more recourse to extreme measures. Fines were levied on Catholic towns, some of which, however, were remitted by the king. It was represented to Salisbury (1609) that the Catholics had grown much more bold even in Dublin, that in the country they drew thousands to "their idolatrous sacrifices, and that the Jesuits stir up the forces of disloyalty." The writer of this letter recommended that the fine of twelve pence should be exacted off the poor every time they absented themselves from religious services, that so much should be levied off the rich as would suffice to repair all the churches and build free schools in every county, and he himself undertook to pay £4,000 a year for the right to collect the fines of the "Recusants" in Munster, Leinster, and Connaught, provided only that he could count on the support of the ecclesiastical and civil authorities.[21] In the following year Chichester informed the authorities in England that "the mayors of cities and towns for the most part refused to take the oath of supremacy, as did also the sheriffs, bailiffs, etc.," and he inquired in what manner he should act towards them. To put an end to this state of affairs Andrew Knox was sent over to Ireland as Bishop of Raphoe, and was commissioned to take measures to stir up the Protestant bishops and to suppress Popery. On his arrival he found that he had a heavy task before him. In a letter to the Archbishop of Canterbury (1611) he wrote that there were only four men in the ministry "who have knowledge or care to propagate the Evangell." "The defection," he wrote, "is so great of those who sometime professed the truth, that where hundreds came to several churches before, there resort now scarce six; the gathering and flocking in great numbers of Jesuits, seminary priests, friars, and gidding Papists of all sorts are so frequent from Rome and all parts beyond the seas, that it seems to him the greatest lading the ships bring to this country are burdens of them, their books, clothes, crosses, and ceremonies; natives and others in corporate towns publicly profess themselves their maintainers. There is no diocese but it has a bishop appointed and consecrated by the Pope, nor province that wants an archbishop, nor parish without a priest, all actually serving their time and the Pope's direction and plenteously maintained by the people, so that the few ministers that are, and bishops that profess to do any good, profit no more than Lot did in Sodom. And sure it may be expected that if God, the king, and his Grace prevent not this unnatural growth of superstition, the face of the kingdom will be shortly clad with this darkness."[22]

He lost no time in summoning a meeting of the bishops (1611), most of whom, according to him, were not very reliable. The Archbishop of Dublin (Jones) was "burdened with the cares of state;" the Archbishop of Armagh was "somewhat old and unable;" the Archbishop of Cashel (Magrath) was "old and unable, whose wife and children would not accompany him to the church;" the Archbishop of Tuam was "well willed and best learned, but wanted maintainers and helpers," and the Bishops of Waterford and Limerick were described as "having no credit." In accordance with the instructions that had been forwarded to them by the king, they agreed that they would take common action for "the suppression of papistry and the plantation of religion;" that they would observe the law of residence in their several dioceses; that they would make visitations every year of their parishes, and inquire into the condition of the churches and the behaviour of their ministers; that by authority of his Majesty's commission they would "carefully tender the oath of allegiance to every nobleman, knight, justice of the peace, and other officers of corporate towns," and make a return to the Lord Deputy of those who took the oath as well as of those who refused it; that they would admit no cleric "to any spiritual promotion" who would not willingly take the oath of supremacy, and that they would inquire in every deanery "what persons receive or harbour trafficking priests, Jesuits, seminaries and massing priests, and friars, and will present their names together with the names of the said priests and Jesuits to the Lord Deputy."[23]

A royal proclamation was issued (1661) ordering all Jesuits and priests to depart from the kingdom immediately; the laity were commanded to attend the Protestant service under threat of severe penalties, students in foreign colleges were ordered to return at once, and Catholic schoolmasters were forbidden to teach within the kingdom. Backed by all the powers of the crown, Knox and his fellow bishops set up a terrible inquisition in every part of the country, and spared no pains to hound down the clergy and those who entertained them, to drive the poorer classes by brute force into the church, to harass the better classes by threats and examinations, and to wipe out every vestige of the Catholic religion. Cornelius O'Devany, a Franciscan, who had been appointed Bishop of Down and Connor (1582), was arrested together with a priest who accompanied him, was tried in Dublin, and was hanged, drawn, and quartered (1612).[24] Almost at the same time the Protestant Bishop of Down and Connor was accused of "incontinence, the turning away of his wife, and taking the wife of his man-servant in her room, subornation of witnesses," and alienation of the diocesan property. He fled from his diocese, was arrested, degraded, and died in prison. The Archbishop of Glasgow and Bishop Knox of Raphoe, himself a Scotchman, hastened to London to secure the appointment of one of their countrymen as his successor; but Chichester wrote that though he would not say that Scotchmen were not good men, he could aver that they were "hot-spirited and very griping" and "such as were not fit for these parts."[25] Several attempts were made to arrest Dr. Eugene Matthews or MacMahon, who had been transferred (1611) by the Pope from Clogher to the Archbishopric of Dublin. He was detested especially by the government, because it was thought that he owed his promotion to the influence of O'Neill, who was also suspected of having had a voice in the appointment of the learned Franciscan, Florence Conry to Tuam (1609).[26] During the course of these years jurors were threatened by the crown lawyers with the Star Chamber unless they found a verdict of guilty, and were sent to prison for not returning a proper verdict against those accused by the Protestant ministers of not attending church; wards of court though Catholic were committed to the guardianship of Protestants, and in every grant a special clause was inserted "that the ward shall be brought up at the college near Dublin (Trinity College) in English habit and religion;" the Irish were excluded from all offices; men of no property were appointed as sheriffs; and the fines for non- attendance at church were levied strictly. Instead of being applied to the relief of the poor they found their way, according to the Catholic Lords of the Pale, into the pockets of the ministers. In reply to this last charge Chichester asserted that they were not given to the poor, because all the poor were recusants, but they were employed "in the rebuilding of churches, bridges, and like charitable purposes."[27]

Yet Knox did not succeed in uprooting the Catholic faith in Ireland. According to a report furnished (1613) to the Holy See by Mgr. Bentivoglio, Internuncio at Brussels, whose duty it was to superintend affairs in Ireland, heresy had made little progress even in the cities, while the nobility and gentry were nearly all Catholic. There were then in Ireland about eight hundred secular priests, one hundred and thirty Franciscans, twenty Jesuits, and a few Benedictines and Dominicans, of whom the Franciscans were held in special esteem. The best of the secular clergy were those who came from Douay, Bordeaux, Lisbon, and Salamanca.[28] In the following year (1614) Archbishop Matthews of Dublin held a provincial synod at Kilkenny at which many useful regulations were made regarding the conduct of the clergy, preaching, catechising, the celebration of Mass, the administration of the sacraments, the relations between the secular and regular clergy, the reading of controversial literature, and the observance and number of fast-days and holidays.[29] In the province of Armagh Dr. Rothe, acting under authority received from Peter Lombard, convoked a provincial synod at Drogheda (1614). It was attended by vicars from the several dioceses and by representatives of the various religious orders, and passed regulations somewhat similar to those enacted at Kilkenny. In both synods the clergy were warned to abstain from the discussion of state affairs and from disobedience to the civil rulers in temporal matters. At Drogheda the new Oath of Allegiance framed by James I. was condemned as being opposed to faith and religion; Catholics were commanded not to have recourse to prevarication or wavering in regard to it, but to reject it openly, and were warned against attendance at divine worship in Protestant churches even though they had previously made a declaration that they meant only to pay a mark of respect to the civil rulers.[30] At the same period the Franciscans and Dominicans founded new colleges on the Continent, at Douay and Lisbon, to supply priests for their missions in Ireland.