After Clontibert and after having proclaimed himself the O'Neill, Hugh O'Neill was branded a traitor and "the principal and chief author of this rebellion and a known practiciser with Spain and her Majesty's other enemies." The events in Ireland soon had an international dimension. Seven years earlier the Spanish Armada had posed a severe threat of invasion from which England was spared only by stormy weather. Accordingly, any indication that rebellious elements in Ireland might invoke the assistance of the Spanish, as had the Munster Geraldines, was regarded as a major threat to England, as well as to the English law and institutions imposed on Ireland. O'Neill was undoubtedly reaching out to both the Spanish king, Philip II, and to the pope, Clement VII, for support in what was presented as a struggle for Irish Catholicism. In 1595 he had appointed the bishop of Killaloe to champion O'Neill's case before the pope and to ask that he repeal the 12th-century papal bull that had granted dominion over Ireland to Henry II. The bishop claimed that the princes and bishops of Ireland were willing to regard O'Neill as their rightful king by right of descent.
O'Neill and his associates made clear the religious character of the impending struggle by an appeal of July 6, 1596, to the chieftains in Munster to join in making war on the English in defense of "Christ's Catholic religion." However, the Old English did not respond, as they were uncertain of the sincerity of O'Neill's religious claims. The same reasoning inhibited papal endorsement until late 1599, when Peter Lombard, the Irish scholar in Louvain, as O'Neill's personal representative in Rome, succeeded in persuading Clement VII of the validity of the cause. The following year the pope offered a plenary indulgence to anyone assisting O'Neill in what was regarded as a struggle comparable to the European wars against the Turks.
Another intriguing component to the story was O'Neill's having visited and been received kindly by James VI, king of Scotland, whose nation was independent of England at this time, even though he was the probable successor to his cousin Elizabeth as English monarch. James had hinted he would favorably treat O'Neill after the death of Elizabeth. The fact that James was the son of Mary, Queen of Scots, the candidate of the Catholic opponents of Elizabeth's reign, made him appear to O'Neill, and probably the pope, as a potential ally regardless of James's own uncertain religious position.
O'Neill took advantage of a lengthy truce to increase his forces and seek foreign assistance. But by the middle of 1597 the government went on the offensive, making a three-pronged march on O'Neill. Both Irish and Old English, such as Donough O'Brien, earl of Thomond and Baron Inchiquin, and Ulick, earl of Clanricard, led other forces in the march. But O'Neill's armies defeated all three movements. After another truce the government went on the offensive again in July 1598, as Sir Henry Bagenel, O'Neill's brother-in-law, led an army of 4,300 northward. On August 15, 1598, O'Neill and O'Donnell, commanding 8,000 men, completely defeated the English, killing a third of their army, included Bagenel. All appeared open for O'Neill to sweep to total victory as supporters from among those defeated in Munster two decades previously rallied to his banner.
However, many, especially those in Connacht and Clare and including some in Munster, appeased by the composition policy, remained unsympathetic. Apprehensive about the situation in Ireland, the queen sent her favorite, Sir Robert Devereux, the earl of Essex, who had promoted the colonial policies that included the brutal slaughter on Rathlin Island in 1574, as lord lieutenant in Ireland. He arrived in April 1599 accompanied by a force of 17,000. But Essex dissipated his forces in a number of different moves and was routed in all engagements, including near Maryborough in Queens or Laois County, in Glen-malure in Wicklow, and in the Curlew Mountains in Connacht. After a further encounter in Monaghan-Louth, he entered into a truce with O'Neill. The outraged queen ordered his return to England in September and a year later he was beheaded.