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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 ā120,000 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]