Though the Dublin parliament (1560) under Elizabeth was dissolved "by reason of its aversion to the Protestant religion," yet the Acts credited to it restored the royal supremacy and en joined the use of the Book of Common Prayer. Offending clergy were threatened with deprivation and perpetual imprisonment, and the laity were to be fined twelve pence (12/— in 1914 value) for non-attendance at Protestant service. With the exception of Curwen of Dublin, and probably two or three others, it cannot be proved that the bishops were disloyal to their trust, and the people clung tenaciously to their religion. Even in the Pale the Government did not press matters to extremes, for the chief gentlemen were still Catholics, and Elizabeth required them for her attacks against Shane O'Neill and other chiefs. The (coming of Father Wolf, S.J. as papal envoy to Ireland to organise the Church, the deputation to Rome and Spain for help, the Bull of Excommunication of Elizabeth (157o), and the landing of James Fitzmaurice, cousin of the earl of Desmond at Dingle (1579) served to harden Elizabeth. From 1580 the persecution was car ried on with great bitterness, and many bishops, priests, and lay men were thrown into prison where they died in chains or were hanged, not for treason, as was ingeniously made to appear, but for their religion. The churches were allowed to go into ruins by Elizabeth's lessees ; some English clergy, chiefly of "bad note," took charge of the cures, and Trinity college was founded (1595) as a bulwark of Protestantism. With the failure of the Spanish expedition at Kinsale (16o1) the Catholic cause was in a parlous condition.
The expected toleration from James I. was not forthcoming. Nay more, all priests were ordered to leave the country (1605). A Star Chamber imposed such heavy fines on conscientious Cath olics that the Catholic noblemen petitioned against these acts of intolerance, but many of them were thrown into prison. They were afterwards granted toleration in return for their support against the northern chiefs and for their approval of the confisca tion of Ulster. The plantation of English and Scottish settlers drove the Catholic population out of the north (1609). Thous ands of acres were appropriated for the support of Protestant schools and of Trinity college, Protestant bishops were urged to suppress popery, and inquisitions were set up in every part of the country. In spite of all, about a thousand priests were known to be carrying on their pastoral work, but Catholics were forbidden to teach school and Catholic parents to send their children abroad.
In the opening years of Charles I. the persecution was less violent. Chapels were opened in the large cities, the Jesuits opened a Catholic university in Back lane, Dublin, the "Graces" were granted for a subsidy, and fines for non-attendance at church were not to be levied. But the persecution broke out again (1629),
and the troops destroyed altars and imprisoned priests. The war of 1641 saw the Ulster lands restored to their former owners, but the wild stories of Protestant massacres are without any solid foundation. The agreement of the Anglo-Irish of the Pale with Ormond (1646), abolishing the oath of Supremacy, removing statutory and educational disabilities, and opening all civil and military offices to Catholics, did not satisfy the majority of the Supreme Council of the Catholic Confederates, including the Papal Legate, Rinuccini, and so Owen Roe O'Neill continued the war.
The situation was now obscured by the arrival of Cromwell to crush both Catholics and Royalists. Wholesale slaughter filled his ten months in Ireland, Drogheda and Wexford suffering most. Priests were shipped abroad, and later in crowds to the Island of Aran, and the Catholic people were transplanted to Connaught. The soldiers were paid the arrears of their pay by grants of farms or estates. Under the Restoration of Charles II. (1660) the clergy returned, the Holy See filled many vacant Sees, and the Catholics as a body enjoyed comparative calm. Consequent, however, on the infamous story of the Popish Plot bishops were ordered to depart the country within a month (1678). After the accession of James II. (1685) a Dublin Parliament granted lib erty of conscience to all (1689), but the battles of the Boyne, Aughrim, and Limerick put an end to James's hopes. The Treaty of Limerick, ratified by William and Mary (1692), granting free dom of religion to Catholics as enjoyed under Charles II., was rejected by the Dublin parliament embittered by the bigotry of the Protestant bishop of Meath, and Catholics were excluded from parliament. Lord Capel brought over with him a bill to secure the Protestant settlement by a system of penal laws framed to uproot the Catholic religion, to drive Catholics out of all offices of power and emolument, and to bestow the lands and offices on the Protestant minority, a sixth of the population. (See IRELAND.) Returns of names and abodes of all priests were made by the revenue officers (1697). The accession of Queen Anne (1702) led to a still more violent persecution, priests as a body refused to take the Oath of Abjuration, wholesale arrests were made and spies employed to track them down (1709). Under George II. (1727-60) persecution began to abate, but at the suggestion of Primate Boulter Catholics were deprived of the vote at parlia mentary and municipal elections. Barristers and solicitors were not admitted to practice unless they had taken oaths that no Catholic could take, mixed marriages were null and void, and the priest celebrating such was guilty of felony (the death penalty was decreed later). At this time there were about 3,00o priests in Ireland.