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 instructed to travel about continually, to which end the castles of Roscommon, Athlone, Monasteroris, Carlow, Ferns, Enniscorthy, and the two forts of Leix and Offaly were placed at his disposal 'either for his pleasure or recreation, or for defence of the countries, punishment of malefactors, or ministration of justice' (Cal. Carew MSS. i. j 273). On 14 June he set out towards Limerick to the assistance of Conor O'Brien, third earl of Thomond [q. v.] The latter was waging an unequal conflict with his uncle Donnell, who had succeeded in getting himself inaugurated O'Brien. He reached Limerick on the 20th, and received the formal surrender of the city. Donnell O'Brien alone of the chieftains of Munster and Thomond failed to pay his respects to the representative of the crown. He was thereupon proclaimed a traitor, and Sussex reinstated his nephew, Conor O'Brien, in his possessions. On 12 July Sussex set out for Galway, and, having confirmed the city charters, shortly afterwards marched to Dublin by way of Leighlin.

After a brief sojourn in the metropolis, he prepared to carry out his instructions for checking the incursions of the Hebridean Scots, and, thinking the best way to attain ' his object was to attack them in their own country, he shipped his army on board the fleet at Lambay, and sailed from Dublin on 14 Sept. Five days later he reached Cantire, 'where I londed and burned the hole countrye.' 'From thens I went to Arren and did the lyke there, and so to the Isles of Cumbras, which I also burned.' His intention of landing on Islay was frustrated by a storm, which drove him to seek shelter in Carrickfergus Haven. Here he landed his men, and made a sudden inroad on the Scots in the Glynnes and Route, and, having burned several villages, returned laden with plunder to Carrickfergus, and thence, on 8 Nov., to Dublin. His expedition had not proved as successful as he had expected, but he begged the queen not to impute his failure to lack of zeal.

On the arrival in Ireland of the news of Queen Mary's death, Sussex placed the government in the hands of Sir Henry Sidney and sailed for England on 13 Dec. By the late queen's will he had been appointed one of her executors with a legacy of five hundred marks, but there was considerable doubt in the minds of the chiefs of the catholic party as to his sympathy with her religious policy (cf. Cal. Simancas MSS. Eliz. i. 25). At the coronation of Queen Elizabeth on 15 Jan. 1559 he officiated as chief sewer by hereditary right. He was one of the peers who sat in judgment on Thomas, lord Wentworth, for the loss of Calais on 22 April, and his name appears as a witness to the signatures to the treaty of Cateau Cambresis. On 3 July he was reappointed lord deputy of Ireland. His instructions closely resembled those formerly delivered to him, but in consequence of the debts incurred by the crown under Mary, he was required to be chiefly careful 'to stay that our realm in quiet, without innovation of anything prejudicial to our estate;' especially he was to try and patch up matters with Shane O'Neill and Sorley Boy MacDonnell (Cal. Carew MSS. i. 284-8). He landed near Dalkey on Sunday, 27 Aug., and three days later he took the oath and received the sword of state in Christ Church. The litany and Te Deum were sung in English, and in this way the protestant ritual was quietly reintroduced by him. Parliament met on 12 Jan. 1560, and was dissolved on 1 Feb., but before it separated acts were passed for restoring the spiritual supremacy of the crown, for uniformity of common prayer and service in the church, for restitution to the crown of first-fruits and twentieths, for confirming and consecrating archbishops and bishops within the realm, for repealing the recent laws against heresy, and for the recognition of the queen's title to the crown of Ireland.

A fortnight later Sussex repaired to England, leaving the government to Sir William Fitzwilliam. He met with a gracious reception from the queen, and was one of the brightest and gayest of the youthful noblemen that thronged her court. On 28 April he jousted in company with Lord Robert Dudley, the Earl of Northumberland, Lord Hunsdon, and others. His commission as viceroy of Ireland was renewed on 5 May. As a special mark of her esteem the queen constituted him lieutenant-general, instead of, as formerly, lord deputy, 'being our cousin in nearness of blood, and an earl of this our land.' His instructions touched, with other matters, the speedy plantation of Leix and Offaly, the recognition of Sorley Boy MacDonnell's claims on condition of his becoming an 'orderly subject' and being willing to hold his lands from the English crown, and the reduction, by fair means or by foul, of Shane O'Neill (ib. i. 291-6). The situation was critical. The generally disturbed state of Ulster, the threatened combination between Shane O'Neill and the Scots, the escape of Brien O'Conor from Dublin Castle, the uncertain attitude of the Earl of Kildare, the return of Teige and Donough O'Brien, and the defeat recently inflicted by them, with the assistance of the Earl of Desmond,