At first the idea was to remove the native population entirely from Leinster and Munster lest the soldiers and "adventurers" might be contaminated， and stern measures were taken to prevent any of the officers or men from taking Irish wives. Ireton laid it down that any officer or soldier who dared to marry an Irish girl until she had been examined by a competent board to see whether her conversion flowed "from a real work of God upon her heart，" should be punished severely.[67] But later on petitions poured in from the new Protestant landowners to be allowed to keep Catholics as servants and labourers， and on the understanding that the masters would utilise this opportunity to spread the true religion， their requests were granted.
Some obtained dispensations or at least managed to secure delays；others probably were able to come to terms with the soldiers to whom their farms had fallen in the general lottery， and others still preferred to risk the danger of transportation by remaining in their own district rather than to seek a new home. Had the Protectorate lasted long enough the policy of transplanting might have succeeded， but as it was the Cromwellian planters soon disappeared or became merged into the native population， and in spite of all the bloodshed and robbery， the people of Ireland generally were as devoted to the Catholic religion in 1659 as they had been ten years before.[68]
When it became clear from the course of events in England that Charles II. was about to be restored to the throne Lord Broghill and Sir Charles Coote， both of whom had helped to crush the Irish Royalists and had profited largely by the Revolution， hastened to show their zeal for the king's cause. The Catholics who had fought so loyally for his father hoped that at last justice would be done to them by re-instating them in the lands from which they had been driven by the enemies of the king. But Charles was determined to take no risks. He sent over the Duke of Ormond， the most dangerous enemy of the Catholic religion in Ireland， as Lord Lieutenant (1660). A Parliament was called in 1661， and as the Catholics had been driven from the corporate towns during the Cromwellian régime and as the Cromwellian planters were still in possession， the House of Commons was to all intents and purposes Protestant. An Act of Settlement was passed whereby Catholics who could prove their "innocence" of the rebellion were to be restored， but the definition of innocence in the case was so complicated that it was hoped few Catholics， if any， would succeed in establishing their claims (1661). A Court of Claims composed of five Protestant Commissioners， was set up to examine the individual cases， but in a short time， when it was discovered that a large number of Catholics were succeeding in satisfying the conditions laid down by law for restoration to their property， an outcry was raised by the planters， and the Court of Claims was suspended (1664). The Act of Explanation was then passed to simplify the proceedings， as a result of which act two-thirds of the land of Ireland was left in the hands of the Protestant settlers. Close on sixty of the Catholic nobility were restored as a special favour by the king， but a large body of those who had been driven out by Cromwell were left without any compensation.
In consequence of the Cromwellian persecution nearly all the bishops and a large body of the clergy， both secular and regular， had been driven from Ireland， but after the accession of Charles， who was known to be personally friendly to the Catholics， many of them began to return. It would be a mistake， however， to imagine that the persecution had ceased， or that the laws against the clergy were not put in force in several districts. Ormond returned to Ireland as hostile to Catholicity as he had been before he was driven into exile；and as he thought that he had a particular grievance against the Irish bishops he was determined to stir up the clergy against them， to divide the Catholics into warring factions， and by favouring one side to create a royalist Catholic party as distinct from the ultramontane or papal party. For this work he had at hand a useful instrument in the person of Father Peter Walsh， a Franciscan friar， who had distinguished himself as a bitter opponent of the nuncio and as a leader of the Ormondist faction in the Supreme Council. In 1661 it was determined by some leading members， both lay and clerical， to present an address of welcome to Charles II.， but by the influence of Walsh and others the address， instead of being a mere protestation of loyalty， was framed on the model of the Oath of Allegiance (1605)， which had been condemned more than once by the Pope. Many of the Catholic lords indicated their agreement with this address or Remonstrance， as it was called， and some of the clergy， deceived by the counsels of Father Walsh， expressed their willingness to adhere to its terms. Ormond， who spent money freely in subsidising Walsh and his supporters，[69] had good reason to be delighted with the success of his schemes. Grave disputes broke out among the clergy， which the government took care to foment by patronising the Remonstrants and by wreaking its vengeance on the anti-Remonstrants on the grounds of their alleged disloyalty. To bring matters to a crisis it was arranged by Walsh and Ormond that a meeting of the bishops， vicars， and heads of religious orders should be held in Dublin (June 1666). In addition to Dr. O'Reilly， Archbishop of Armagh， Bishops Plunkett of Ardagh， and Lynch of Kilfenora， there were present a number of vicars of vacant dioceses together with representatives of the Franciscans， Dominicans， Augustinians， Capuchins， and Jesuits.[70] Dr. O'Reilly spoke strongly against the terms of the Remonstrance as being highly disrespectful to the Pope， and the majority of those present supported his contention.