After the short incumbency of Donagh O'Tighe (1560-62), the see was filled by Richard Creagh (1564-85), a native of Limerick . He was arrested by order of Queen Elizabeth and imprisoned by her in the Tower of London, where he was tortured and maltreated and left to languish in captivity for eighteeneyears till his death. Edward Mac Gauran, who succeeded him (1587-94), was very active in soliciting aid from the pope and the king of Spain for the Irish who were then engaged in a struggle for liberty of conscience with the English Queen. After an interval of eight years, he was succeeded by Peter Lombard (1601-25), one of the most learned men of his time. He remained in exile, in Rome, during the whole twenty-four years of his incumbency and thus never once visited his diocese. Hugh Mac Cawell, a Franciscan, was consecrated abroad for the see in 1626, but died before he could reach it. Hugh O'Reilly, the next primate (1628-53), was very active in the political movements of his day. In 1642, he summoned the Ulster bishops and clergy to a synod at Kells in which the war then carried on by the Irish was declared lawful and pious. He took a prominent part in the Confederation of Kilkenny and was appointed a member of the Supreme Council of twenty-four persons who carried on the government of the country in the name of King Charles I. After the defeat and death of most of the Catholic Irish chieftains he was elected generalissimo of the Catholic forces and prolonged the heroic though hopeless conflict. Edmund O'Reilly (1657-69) succeeded to the see, but owing to the difficulties of the time was only able to spend two years in the diocese out of the twelve of his incumbency. He was exiled on four different occasions. During the whole time he spent in the diocese, he was hiding in woods and caves and never had any bed but a cloak thrown over straw. He suffered a great deal from the machinations of the notorious Father Walsh, the author of the "Loyal Remonstrance" (1661, 1672) to King Charles II, and died in exile in France.

The next primate was the Venerable Oliver Plunket (1669-81), the cause of whose beatification is at present being promoted. Shortly after his accession to the see, he was obliged to defend the primatial rights of Armagh against the claims put forward for Dublin by its archbishop, Dr. Peter Talbot. At a meeting of the Catholic clergy in Dublin in 1670, each of these prelates refused to subscribe subsequent to the other. Dr. Plunket thereupon wrote a work on the ancient rights and prerogatives of his see, published in 1672, under the title "Jus Primatiale; or the ancient Pre-eminence of the See of Armagh above all the other Archbishops in the Kingdom of Ireland, asserted by O. A. T. H. P". This was replied to two years later by Dr. Talbot in a dissertation styled "Primatus Dublinensis; or the chief reasons on which the Church of Dublin relies in the possession and prosecution of her right to the Primacy of Ireland". A violent persecution stilled the controversy for some time and subsequent primates asserted their authority from time to time in Dublin. In 1719 two Briefs of Clement XI were in favour of the claims of Armagh. Still the matter was not allowed to rest and Dr. Hugh Mac Mahon felt compelled to write a work treating the subject exhaustively in answer to an anonymous pamphlet published by Father John Hennessy, a Jesuit of Clonmel. Dr. Mac Mahon's work, written under great difficulties, appeared in 1728 under the title of "Jus Primatiale Armacanum; or the Primatial Right of Armagh over all the other Archbishops and Bishops and the entire clergy of Ireland, asserted by H. A. M. T. H. P". This learned work contains the last word on the subject and is conclusive. In practice, however, the primatial right has fallen into desuetude in Ireland as in every other part of the Church.

In 1679, Venerable Oliver Plunket was arrested on a ridiculous charge of conspiring to bring 20,000 Frenchmen into the country and of having levied moneys on his clergy for the purpose of maintaining 70,000 men for an armed rebellion. After being confined in Dublin Castle for many months, he was presented for trial on these and other charges in Dundalk; but the jury, though all Protestants, refused to find a true bill against him. The venue, however, of his trial was changed by his enemies to London, where he was tried by an English jury before he was able to gather his witnesses and bring them across, though he made the request to the judge. The principal witnesses against him were some disreputable priests and friars of Armagh whom he had censured and suspended for their bad conduct. He was dragged on a sledge to Tyburn on 1 July, 1681, where he was hanged, drawn, and quartered in presence of an immense multitude. His head, still in a good state of preservation, is in the possession of the Dominican nuns of Drogheda.

During this trying period, the primates had to live in the greatest obscurity in order to disarm the malice of the enemies of the Catholic clergy. Dominic Maguire (1683-1707), a Dominican, succeeded to the see after the death of the Venerable Oliver Plunket. This primate, having to go into exile after the surrender of Limerick in 1691, spent the sixteen years that intervened between that time and his death in a very destitute condition. In the meantime the See of Armagh was administered by a vicar, Patrick Donnelly, a priest of the diocese, who in 1697 was appointed Bishop of Dromore, though retaining the administration of Armagh for several years afterwards. His name occurs in the government register of the "popish clergy" of Armagh, made in 1704, as the pretended popish priest of that part of the parish of Newry that lies in the county of Armagh. The sureties for his good conduct were Terence Murphy of Lurgan and Patrick Guinnisse of the same town. Altogether the names of nineteen parish priests appear on the register for the county of Armagh. From the returns made in 1731 by the Protestant archbishops and bishops regarding the growth of popery in Ireland, we find that in the Diocese of Armagh there were 26 Mass-houses, 77 officiating priests, 5 friaries, 22 friars, 1 nunnery with 9 nuns, 7 private chapels and 40 popish schools. Owing to the severity of the laws there was no primate resident in Ireland for twenty-three years after the flight of Primate Maguire, in 1691. Hugh Mac Mahon (1714-37), Bishop of Clogher, was at last appointed to the bereft see. Living during the worst of the penal times, the primate was obliged constantly to wander from place to place, saying Mass and administering Confirmation in the open air. Nevertheless, in spite of these difficulties he has left his name to posterity by the learned work "Jus Primatiale Armacanum", written by command of the pope in defence of the primatial rights of Armagh. He was succeeded by his nephew, Bernard Mac Mahon (1737-47), then Bishop of Clogher, who is described as a prelate remarkable for zeal, charity, prudence, and sound doctrine. He also suffered considerably from the persecution, and spent most of his time in hiding. Bernard was succeeded in the primacy by his brother, Ross Mac Mahon (1747-48), also Bishop of Clogher. Michael O'Reilly (1749-58), Bishop of Derry, was the next primate. He published two catechisms, one in Irish and the other in English, the latter of which has been in use in parts of the north of Ireland till our own time. On one occasion this primate and eighteeneof his priests were arrested near Dundalk. He lived in a small thatched cottage at Termonfechan, and at times had to lie concealed in a narrow loft under the thatch. Anthony Blake (1758-86) was his successor. The persecution having subsided to a great extent, he was not harried like his predecessors, but nevertheless could not be induced to live permanently in his diocese, a circumstance which was the occasion of much discontent among his clergy and led to a temporary suspension from his duties. Richard O'Reilly (1787-1818) was his successor in the primacy. Having an independent fortune, he was the first Catholic prelate since the Revolution who was able to live in a manner becoming his dignified station. By his gentleness and affability he succeeded in quieting the dissensions which had distracted the diocese during the time of his predecessor and was thenceforward known as the "Angel of Peace". In 1793, he laid the foundation-stone of St. Peter's Church in Drogheda, which was to serve as his pro-cathedral, one of the first Catholic churches to be built within the walls of a town in Ireland since the Protestant Reformation. The Protestant Corporation of Drogheda, wearing their robes and carrying the mace and sword, appeared on the scene and forbade the ceremony to proceed, but their protest was disregarded.

Hugh Goodacre, the first Protestant prelate who presided over the diocese, was appointed by Edward VI, in 1552. He was consecrated according to the Protestant ordinal and survived his consecration only three months. Adam Loftus (1563-67), from whom the Irish Protestant hierarchy claim to derive their orders, was consecrated by Hugh Curwin, Archbishop of Dublin, according to the form annexed to the second Book of Common Prayer of the time of Edward VI. The most learned of the Protestant primates was James Ussher (1625-56), whose most important works were "Veterum Epistolarum Hibernicarum Sylloge", published in 1632, and "Brittanicarum Ecclesiarum Antiquitates", which appeared in 1639. He left his valuable library, comprising several thousand printed books and manuscripts, to Trinity College, Dublin, and his complete works were published by that institution in twenty-four volumes at the cost of 3,000. In spite of his learning, this prelate's character was marked by a most intolerant spirit of bigotry against the Irish Catholics. His judgment against toleration of Papists, i.e. "to consent that they may freely exercise their religion and profess their faith and doctrine is a grievous sin", was a signal for the renewal of persecution and led to the Rising of the Irish Catholics in 1641. John Bramhall (1660-63), another learned Protestant divine, succeeded Ussher. His works on polemic and other subjects have been published in four folio volumes. Narcissus March (1702-13), another learned prelate, built the noble library of St. Sepulchre's in Dublin, which bears his name, filled it with a valuable collection of theological and Oriental works and liberally endowed it for the support of a librarian and deputy. Hugh Boulter (1724-42), John Hoadly (1742-46), and George Stone (1746-64) are principally famous as politicians and upholders of the "English Interest" in Ireland. The first two supported and promoted the penal laws against the Catholics, but Stone was opposed to persecution. Richard Robinson, first Baron Rokeby (1765-94), raised Armagh by his munificence from extreme decay to a state of opulence and embellished it with various useful public institutions. He built an episcopal palace, a public library, an infirmary, and an observatory. Lord John George Beresford (1822-62) was also distinguished by his munificence. He restored Armagh Cathedral at a cost of 34,000 and is said to have spent 280,000 in acts of public benevolence. On his successor, Marcus Gervais Beresford (1862-65), fell a large portion of the task of providing for the future organization and sustentation of the Protestant Episcopal Church in Ireland, which was disestablished from 1 January 1871. After the flight of the Earls Ó Neill and O'Donnell, large portions of their forfeited estates were made over to the Protestant see, which, together with the land previously belonging to the see in Catholic times, made up a total of 100,563 acres, producing in modern times a gross revenue for the Protestant primate of 17,670. By the Church Temporalities' Act of 1833, this was considerably reduced, and the net income of the see before the disestablishment was 12,087. Since that event the primate receives an annual salary from the Church Representative Body of 2,500, with the palace free of rent. The glebe lands belonging to the eighty-eight benefices in the diocese comprised 19,290 acres. Since disestablishment, about 9,000 are contributed annually by the voluntary system for sustentation funds and about 5,000 for various other Church purposes.

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