He fell on his knees before the deputy, begging liberty of conscience, free and open exercise of religion, protesting that the people would be ready to resist all foreign invasion were that granted; and finally beseeching that some of the ruined churches might be given to the Catholics, who were ready to rebuild them, and pay for them a yearly rent into his majesty's exchequer.

But the deputy was inexorable, and all he would grant was leave to wear clerical clothes, and celebrate mass in private houses.
Mountjoy entered Waterford, received from the citizens the oath of allegiance, and made over the city churches to the small section of Protestants.

At the same time he sent despatches to other towns ordering the authorities to evict the Roman Catholics from the places of worship.

And then proceeding to Cork, and thence through Cashel to Dublin, he undid all that the clergy had done with respect to the churches, 'leaving perhaps to future statesmen,' writes Father Meehan, 'living above the atmosphere of effete prejudices, the duty of restoring to the Catholics of Ireland those grand old temples, which were never meant to accommodate a fragment of its people.'[1] [Footnote 1: Page 30.] When Mountjoy returned to Dublin he found that he had been created Lord Lieutenant of Ireland with two-thirds of the deputy's allowance, Sir George Carew, appointed deputy during his absence in England, receiving the other third together with his own pay as treasurer-at-war.

Mountjoy was also informed that the royal pardon had been granted to Tyrone under the great seal, and that all other grants made to him by the lord deputy had been confirmed.