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]