But the placing of the acts upon the statute book did not mean that the cause of the king had triumphed. Steps must be taken to enforce the laws against the jurisdiction of the Pope. Already in October 1537 the royal commissioners, who had been sent over by the king to overawe the Parliament, undertook a judicial tour through the south-eastern portion of Ireland to inquire into the grievances of the people, and especially to secure grounds of complaint against the ecclesiastics, so as to enable the government to overcome the opposition of their representatives in Parliament. During their journey they held sessions at Kilkenny, Waterford, Wexford, New Ross, Clonmel, and Tipperary. In the circumstances it is not difficult to understand how easy it was for them to find individuals ready to come forward with accusations both against the lay lords and the clergy, especially as the commissioners in some cases at least suggested the points of complaint. In Wexford, for example, the crime alleged against the Dean of Ferns and three other priests of having "pursued" Bulls from Rome has a very suspicious ring. Against many individual clerics, including the Archbishop of Cashel and the Bishop of Waterford, the priors and heads of several religious houses and certain rectors and vicars, it was alleged that they levied various exactions like the lay lords, that they demanded excessive fees on the occasion of their ministrations, and that they asserted claims to fishing weirs, etc., to which they were not entitled. If it be borne in mind that the bishops, priors, and heads of religious houses were also landlords like the lay lords, against whom charges of almost similar exactions were lodged, the presentments of grievances at least in this respect were not very convincing. For the same reason the fact that the Archbishop of Cashel was said to have been in a boat which robbed a boat from Clonmel and that he caused a riot in the latter city, that the Bishop of Waterford and Lismore took bribes, or that Purcell, the Bishop of Ferns, joined with O'Kavanagh in an attack upon Fethard need not cause any surprise. It was only against James Butler, the Cistercian abbot of Inislonagh and his monks, the Augustinian monks of Athassel, the Carmelite priors of Lady Abbey near Clonmel and Knocktopher, and the abbot of Duisk that grave charges of immorality were made. Even if these charges were true, and the evidence is by no means convincing, they serve only to emphasise the downfall of discipline caused in the individual religious houses by the interference with canonical election, and the intrusion oftentimes by family influence of unworthy men as abbots or commendatory abbots.[6]

Henry VIII. was anxious to complete the conquest of Ireland even before he had broken with the Pope, but after the separation of England from Rome he realised more clearly the dangers that might ensue unless the Irish and Anglo-Irish princes were reduced to submission. As things stood, Ireland instead of contributing anything was a constant source of loss to the royal treasury, and, were an invasion attempted by some of his Continental rivals, Ireland might become a serious menace to England's independence. The complete overthrow of the Geraldine rebellion (1535) had prepared the way for a more general advance, but the failure of the Deputy to capture the young heir to the Earldom of Kildare was as displeasing to the king personally as it was dangerous to his plans. The boy was conveyed away secretly by his tutor, a priest named Leverous, who was advanced afterwards to the See of Kildare, and was brought for safety to the territory of O'Brien of Thomond. When Thomond was threatened by the rapid advance of the Deputy, the young Earl of Kildare was conveyed to his aunt, Lady Eleanor MacCarthy of Cork, who on her marriage to Manus O'Donnell, Prince of Tyrconnell, brought the boy with her to Donegal (1538).

O'Connor of Offaly and O'Carroll had been compelled to sue for peace (1535). In the following year Lord Grey made a tour of the south- eastern parts of Leinster, proceeded through Tipperary, and directed his march against the strongholds of O'Brien of Thomond. Partly by his own skill and boldness, partly also by the treachery of one of the O'Briens, he succeeded in capturing some of the principal fortresses including O'Brien's Bridge. Had it not been for a mutiny that broke out among his soldiers Lord Grey might have succeeded in forcing O'Brien to make terms, but, as it was, he was obliged to desist from further attack and to retreat hastily to Dublin. O'Brien soon recaptured the positions he had lost; O'Connor of Offaly took the field once more, and the unfortunate Deputy, harassed by his enemies on the privy council and blamed by the king for his failure to get possession of the hope of the Geraldines, found himself in the greatest difficulties. But he was a man of wonderful military resource, and knowing well that failure must mean his own recall and possibly his execution, he determined to put forth all his energies in another great effort. So long as the Irish in the Leinster districts were active it was little use for him to undertake dangerous expeditions towards the more remote districts, and for this reason he turned his attention to O'Connor of Offaly. Before many months elapsed he forced the MacMurroughs, the Kavanaghs, the O'Moores, the O'Carrolls, MacGillapatrick of Ossory, and O'Connor to sue humbly for peace.