In 1581, he campaigned against the clans of Kavanagh and O'Toole, and on the 30th of August 1581 was commissioned to follow the lord deputy in the government's campaign against Fiach MacHugh O'Byrne, a rebel leader whose fastness lay in the Wicklow mountains. During that campaign he was engaged at the Battle of Glenmalure in charge of the rear guard, and covered the retreat of Grey's forces after they had been routed from the glens. At the end of the year his troops were discharged, and he went to England to seek further employment from the queen's principal secretary, Lord Burghley.
At the beginning of 1583, Stanley was sent back to Ireland to deal with the rebel Geraldines of Desmond, and was appointed by the Earl of Ormond as commander of the garrison at Lismore; he was also constable of Castlemaine, which he intended to "make a town of English". During this tour of duty he assisted in the pursuit of the earl of Desmond and the seneschal of Imokilly, and in the final subjugation of Munster at the end of the rebellion.
The defeat of the rebels presented many opportunities for advancement to the New English, those adventurers and administrators who had taken advantage of crown policy in Ireland to establish fortunes for themselves outside of their restricted circumstances at home. Stanley became ambitious and sought the presidency of the province of Connacht by petitioning Sir Francis Walsingham and Burghley, but this was denied. Instead, he was made sheriff of Cork in August 1583, and then assumed the government of Munster in the absence of Sir John Norris. He boasted of having hanged 300 rebels and of leaving the rest so terrified that, "a man might now travel the whole country and none molest him".
At the end of 1584, the new lord deputy, Sir John Perrot, sent Stanley north in the company of Sir Henry Bagenal to act against the Ulster chieftains and the Scots led by Sorley Boy MacDonnell. During this campaign he received severe wounds and was laid up for several months. He had marched with two companies to Ballycastle to join up with a troop of cavalry stationed in Bunamargey Abbey (the burial place of the MacDonnells), after Bagenal was forced to take refuge in Carrickfergus. On 1 January 1585, the enemy took him completely by surprise in camp beside the abbey, when half a dozen horsemen at the head of the Scots foot set the thatched roof of the church on fire. Stanley was forced to fight in his shirt, having had no time to don armour, and was wounded in the thigh, the arm and side, and in the back (he claimed he had turned to his men to urge them on). Some of the horse were burned in the abbey, and the enemy fell away without pursuit, and soon after twenty four oared galleys of the Scots rowed across Ballycastle Bay while Stanley's ships remained at anchor in flat calm conditions. Although he subsequently almost defeated Sorley Boy's nephew, reinforcements arrived from Scotland and there was little more to be achieved. Stanley returned to England in October, where his service in Ireland was considered to have been brilliant.
Having raised 1,400 troops - most of them Irish - Stanley set out for the continent. En route he stayed at London, where it was reported that he had been in the confidence of jesuits and privy to part of the Babington plot, and that he had corresponded with the Spanish ambassador, Mendoza, and with the Tower-bound Earl of Arundel. When ordered to carry on to the Netherlands, he tarried in England, supposedly in the expectation of an attempt on Elizabeth's life or the arrival of a Spanish fleet. Eventually he was obliged to sail, but anticipated joining with the Duke of Parma.
In August 1586, Stanley joined Leicester and, with John Norris, took Doesborg in a violent assault. Following his service at Zutphen (when Sir Philip Sidney was fatally wounded), Leicester deemed him worth his weight in pearl; in October, with Sir William Pelham he took Deventer, where he was appointed governor of the city in command of a garrison of his own - mostly Irish - troops, numbering 1,200.
The enmity between Leicester and Norris resulted in a commission for Stanley to act independently of the latter, who had taken over command of the English forces on Leicester's departure, an arrangement that prompted dissent from the Estates General. Stanely promptly communicated with the Spanish governor of Zutphen, and Deventer was surrendered by him to the Spanish in January 1587, whereupon almost the entire garrison entered the Spanish service. This occurred the day after Zutphen had similarly been betrayed by the English commander Rowland York (28 January).
Cardinal William Allen published a letter at Antwerp justifying Stanley's actions and setting out the case for the assassination of Elizabeth I as a heretic, citing the Papal bull Regnans in Excelsis. At the time, the queen had been considering Stanley for honours and titles, including his appointment as viceroy of Ireland; but he was almost certainly in complete sympathy with the jesuits, which order his brother had joined and whose members sang his praises. Thereafter he plotted an invasion of England - the troops to disembark at Milford-Haven and in Ireland, where bases for the larger operation might be established - but he was disappointed at the countenance he received from the Spanish authorities, although they did award him a crown pension (the arrears of which he had to pursue in later years).
By 1595 Stanley was desperate and suffered a reproof from the Spanish governor of the Netherlands for his violent language against Elizabeth. He continued in military service for the Spanish and was opposed to King James I on his accession in 1603, but he soon sued for a pardon and seemed desirous of returning to England. Sir Robert Cecil exonerated him from complicity in the Gunpowder Plot, but he never gained permission to visit England and spent the rest of his life in relative obscurity. He maintained a close association with the Jesuits, and when he had fallen out with them, with the English Carthusians.
Richard Barnfield dedicated his poem Cynthia (a long ode to Queen Elizabeth I) to Stanley in 1595.
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