The surrender of Trim, Dundalk and Ross followed, but at Waterford Cromwell met with a stubborn resistance and the advent of winter obliged him to raise the siege. Next year Cromwell penetrated into Munster. Cashel, Cahir and several castles fell in February, and Kilkenny in March; Clonmel repulsing the assault with great loss, but surrendering on the 10th of May 1650. Cromwell himself sailed a fortnight later, leaving the reduction of the island, which was completed in 1652, to his generals. The re-settlement of the conquered and devastated country was now organized on the Tudor and Straffordian basis of colonization from England, conversion to Protestantism, and establishment of law and order. Cromwell thoroughly approved of the enormous scheme of confiscation and colonization, causing great privations and sufferings, which was carried out. The Roman Catholic landowners lost their estates, all or part according to their degree of guilt, and these were distributed among Cromwell's soldiers and the creditors of the government; Cromwell also invited new settlers from home and from New England, two-thirds of the whole land of Ireland being thus transferred to new proprietors. The suppression of Roman Catholicism was zealously pursued by Cromwell; the priests were hunted down and imprisoned or exiled to Spain or Barbados, the mass was everywhere forbidden, and the only liberty allowed was that of conscience, the Romanist not being obliged to attend Protestant services.
These methods, together with education, "assiduous preaching ... humanity, good life, equal and honest dealing with men of different opinion," Cromwell thought, would convert the whole island to Protestantism. The law was ably and justly administered, and Irish trade was admitted to the same privileges as English, enjoying the same rights in foreign and colonial trade; and no attempt was made to subordinate the interests of the former to the latter, which was the policy adopted both before and after Cromwell's time, while the union of Irish and English interests was further recognized by the Irish representation at Westminster in the parliaments of 1654, 1656 and 1659. These advantages, however, scarcely benefited at all the Irish Roman Catholics, who were excluded from political life and from the corporate towns; and Cromwell's union meant little more than the union of the English colony in Ireland with England. A just administration, too, did not compensate for unjust laws or produce contentment; the policy of conversion and colonization was unsuccessful, the descendants of many of Cromwell's soldiers becoming merged in the Roman Catholic Irish, and the union with England, political and commercial, being extinguished at the Restoration. Cromwell's land settlement--modified by the restoration under Charles II. of about one-third of the estates to the royalists--survived, and added to the difficulties with which the English government was afterwards confronted in Ireland.