The first of these rebellions, that of Shane O’Neill, fully exposed the weakness and later the folly of the government. O’Neill’s father, Conn the Lame (Conn Bacach), who as the “O’Neill” was head of a whole network of clans, had been made earl of Tyrone in 1541, and the succession rights of his illegitimate son Feardorchadh (Matthew) were recognized. Shane, younger but the eldest legitimate son, was elected O’Neill on his father’s death in 1559, and soon afterward Feardorchadh was killed. O’Neill then battled against the Dublin government, demanding recognition according to the laws of primogeniture, and he insisted that neither of Feardorchadh’s sons, Brian and Hugh, had claims to the earldom. Elizabeth invited O’Neill to London to negotiate, but the opportunity for a statesmanlike settlement was lost. O’Neill was to be “captain of Tyrone” and was encouraged to expel from Antrim the MacDonnell (MacDonald or MacConnell) migrants from Scotland. Returning to Ireland in May 1562, O’Neill routed the MacDonnells, as well as the loyal O’Donnells of the northwest, and attempted to secure support from Scotland and France. Eventually the government was saved from a serious situation only through the defeat of O’Neill by the O’Donnells and his murder in 1567 by the MacDonnells.

The lands of the O’Neills and even of loyal Gaelic lords were declared forfeit in 1569, and, in a wave of enthusiasm for colonization, various questionable adventurers were permitted to attempt substantial plantations in Munster, Leinster, and Ulster. The folly of this policy was seen when the government, despite its having declared the position of “O’Neill” extinguished, allowed the O’Neills to elect Shane’s cousin Turlough Luineach as their chief. Butlers and Munster Fitzgeralds also combined forcibly to resist the plantations. The only gleam of statesmanship shown in these years by Henry Sidney, lord deputy (1565–71, 1575–78), was that he managed to avoid a major combination against the government’s religious policy. The Butlers were induced to submit, the planters were given only limited support, and a head-on collision with Turlough Luineach was averted. When the Ulster plantation plans could not be carried out against Irish resistance, the queen wisely decided that they should be dropped. The pardon of the Butlers pacified Leinster, and, although in Munster the earl of Desmond’s cousin James Fitzgerald, called “Fitzmaurice,” attempted to make the war one of religion, he, too, was eventually pardoned.

The Desmond rebellion

Despite his pardon, Fitzmaurice fled to the European continent in 1575, returning to Ireland in 1579 with papal approval for a Roman Catholic crusade against Queen Elizabeth. Although neither France nor Spain supported the crusade and Fitzmaurice was surprised and killed in August 1579, the government was extremely apprehensive. Gerald Fitzgerald, 14th earl of Desmond, then assumed direction of the enterprise. As a military commander he was wholly deficient, and his mediocrity may well have kept outstanding figures in the north and west out of the movement. The rebels were defeated, and in November 1580 a force of Italians and Spaniards was massacred at Dún an Óir (“Golden Fort”), Smerwick Harbour, County Kerry.

The end of the Desmond rebellion gave the government the opportunity to confiscate more than 300,000 acres (100,000 hectares) in Munster and initiate more stringent proceedings against Roman Catholics. But the plantation was not a success. A more statesmanlike attitude was displayed in regard to Connaught land titles. When Sir John Perrot was lord deputy (1584–88), a number of agreements were made with individual landowners and chieftains by which their titles were officially recognized in return for regular fixed payments. This was a step in the process of converting a great part of the country to English tenures. Perrot was less successful in handling the 1585–86 Parliament, in which the government’s anti-Catholic program was defeated by the opposition.

The Tyrone rebellion

The origins of the third rebellion, the O’Neill (Tyrone) war, remain in doubt. Both Hugh Roe O’Donnell and Hugh O’Neill (younger son of Feardorchadh), for whom the earldom of Tyrone had been revived in 1585 and who had been elected O’Neill on Turlough Luineach’s death in 1595, certainly resented the extension of the royal administration, but the religious issue was probably more important. For a generation, exiled Roman Catholics had been trained as missionaries in the continental colleges of the Counter-Reformation, and the majority of those who returned to Ireland concluded that Catholicism could survive there only if Elizabeth were defeated. The outbreak of hostilities in Ulster in 1594 was at first confined to the northwest, where O’Donnell and Maguire, lord of Fermanagh, tried to drive out the English troops. The intervention of Hugh O’Neill was expected, if not inevitable. His participation with his brother-in-law O’Donnell proved decisive in the north and west, and the English were defeated both in Ulster and in Connaught. A more intimidating combination thus threatened Dublin than even in Shane O’Neill’s time. Even in the Pale, arbitrary exactions and exclusion from offices won Hugh much sympathy, and it was said that he knew of Dublin Castle decisions before they were known in the city. Resentful of O’Neill’s alleged ingratitude, Elizabeth became impatient of negotiations with him and finally sent Robert Devereux, 2nd earl of Essex, to Ireland (1599) to subdue him. But Essex lost his reputation by his inglorious progress through the country and by the speed with which he returned to England after a private conversation with O’Neill. Before Charles Blount, Lord Mountjoy, arrived in 1600 to replace Essex, the Irish leaders had gained the qualified support of Pope Clement VIII and of King Philip III of Spain. But Philip could afford to send only a minimal force to aid the Irish rebels. Its leader, Juan del Aguila, occupied Kinsale and was besieged (1601) by Mountjoy. O’Neill marched south to relieve Aguila, but a rash attempt to surprise the English lines by night proved disastrous (December 24, 1601); the Irish were defeated and the Spaniards surrounded. O’Neill held out in Ulster for more than a year but finally submitted a few days after the queen’s death in March 1603.

Viewed generally, Elizabeth’s Irish policy had the distinction of having reduced the country to obedience for the first time since the invasion of Henry II. But her policies had serious costs; the loyalty of the Irish was perennially strained over the religious issue, so that further rebellion was almost inevitable and virtually predictable in 1640 when the English government was embarrassed by the Second Bishops’ War with Scotland. Economically, the towns and the countryside were needlessly exploited by the new administrators and planters, while the queen’s expenditure was substantially increased. Commitments in Ireland were at least partly responsible for the poverty of the crown, which was to become a serious factor in precipitating its 17th-century conflict with Parliament.