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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 1607they 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.