Lord Mountjoy was in a difficult position. He was uncertain as to the religious policy of the king, but in the end he determined to suppress the Catholic movement by force. He marched South to Kilkenny and thence to Waterford, where he had an interview with Dr. White. Everywhere the churches were restored to the Protestants, though it was hinted that the Mass might still be celebrated privately as in the days of Elizabeth. In Cork the condition of affairs was much more serious, and it was necessary to bring up the guns from Haulbowline before the mayor and citizens could be induced to submit. Reports came in from all sides that the country was swarming with Jesuits and seminary priests, that they were stirring up the people to join hands with the King of Spain, and to throw off their allegiance to James I. These rumours were without foundation, as is shown by the fact that most of the towns and cities in Leinster and Munster which were noted as specially Catholic, had not stirred a finger to help O'Neill in his war against Elizabeth. But they were put in circulation to prejudice the mind of King James against his Irish Catholic subjects, and to wean him away from the policy of toleration which he was said to favour. Loftus, Archbishop of Dublin, and Jones, Bishop of Meath, hastened to warn the king against a policy of toleration. They threw the whole blame of the late war on the Jesuits and seminary priests, and cast doubts upon the loyalty of the Catholic noblemen of the Pale. They called upon his Majesty to make it clear "even in the morning of his reign," that he was ready "to maintain the true worship and religion of Jesus Christ," to let the people understand that "he will never permit and suffer that which in his godly zeal he so much abhors, to devise some means of preventing the plots and aims of Jesuits and seminary priests, who "come daily from beyond the seas, teaching openly that a king wanting the Pope's confirmation is not a lawful king," to send over some "learned and discreet preachers" to the principal cities and towns, and to compel the people "by some moderate co-actions to come to church to hear their sermons and exhortations."[3]

As a means of spreading the new gospel amongst the Irish people it was recommended that "a learned ministry be planted, and that the abuses of the clergy be reformed;" that all bishops, Jesuits, seminary priests, and friars should be banished from the kingdom, that no lawyers be admitted to the bar or to the privy council unless they attended the Protestant service, and that all sheriffs, mayors, justices of the peace, recorders, judges, and officials be forced to take the oath of supremacy. Loftus and Jones insisted, furthermore, that Catholic parents should be forbidden to send their children to Douay and Rheims, and should be compelled to send them to the Protestant diocesan schools. They reported that although the Bishop of Meath had opened a school in Trim at great expense to himself, only six scholars attended, and that when the teachers began to use prayers in the school and to show themselves desirous of bringing their pupils to church, the pupils departed, and the teachers, though graduates of the University, were left without any work to do.[4]

As James showed great reluctance to take any active measures against the Catholics, Brouncker, the President of Munster, Lyons, Protestant Bishop of Cork, and the other members of the Council of Munster issued a proclamation (14 Aug. 1604) ordering "all Jesuits, seminaries, and massing priests of what sort soever as are remaining within one of the corporate towns of the province" to leave before the last day of September, and not to return for seven years. Any persons receiving or relieving any such criminals were threatened with imprisonment during his Majesty's pleasure and with a fine of £40 for every such offence, and "whosoever should bring to the Lord President and Council the bodies of any Jesuits, seminaries, or massing priests" were promised a reward of £40 for every Jesuit, £6 3s. 4d. for every seminary priest, and £5 for every massing priest. Fearing, however, that his action might be displeasing to the king, Brouncker took care to write to Cecil that the cities of the South were crowded with seminary priests who said Mass publicly in the best houses "even in the hearing of all men," and that he had delayed taking action till they began to declare boldly that his Majesty was pleased "to tolerate their idolatry."[5]