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 patched into England to acquaint the council with the situation of affairs in Ireland. He returned about the end of January 1563; but appears to have spent the greater part of that year and the beginning of the next in England. In May 1564 Sir Nicholas Arnold, late commissioner for reforming and introducing economy into the Irish government, was appointed lord justice, and having insinuated many things against him as vice-treasurer, which he wholly failed to substantiate, the latter retorted by saying that he could have governed Ireland as well as Arnold and saved the queen twenty thousand marks (State Papers, Eliz., xiii. 57, xviii. 1, 2, 3). Arnold was succeeded by Sir Henry Sidney, and he being summoned home, Fitzwilliam and Dr. R. Weston were on 14 Oct. 1567 sworn lords justices, much against the will of the former, who declared that his last justiceship had cost him 2,000l. This was bad enough, but to be charged by the queen with not preventing the landing of the Scots in Antrim was intolerable, and he complained bitterly against it, protesting that he had for eight years and more truly and faithfully served her majesty without bribery, robbery, or friendly gifts (ib. xxiii. 13). Though ‘not bred up to arms,’ he, in the spring of the following year (1568), undertook an expedition into the north; but it was badly managed, and ended in disgraceful failure (, Ireland, ii. 133). Fortunately Sidney returned in October and relieved him from his more onerous duties. In 1570 he appears to have resided chiefly in England; but on 29 Jan. 1571 he returned to Ireland. In March Sidney departed, and on 1 April he was appointed lord justice. He was suffering severely at the time from ague, and protested his unfitness for the government, and his impoverishment after thirteen years' service, tending to his utter ruin (Ham. Cal. i, 454, 457). His petition, supported by the entreaties of Lady Fitzwilliam, who implored the queen to allow her husband to return to England before the winter came on, was unsuccessful, and instead he was appointed lord deputy, and sworn into office on 13 Jan. 1572 (patent, 11 Dec. 1571).

Forced into the gap against his will, and miserably supplied with money, Fitzwilliam's government (1572–5) was not remarkably successful, though he declared that Ireland in 1575 was in a much better state than it was in 1571 (ib. ii. 49). With Sir Edward Fitton in Connaught and Sir John Perrot in Munster, his attention was chiefly directed to Ulster. Here the grants of land made by Elizabeth to Malby, Chatterton, Sir Thomas Smith, and the Earl of Essex (1572–3), leading as they did to serious complications with the Irish, and with Turlough Luineach O'Neill in particular, greatly added to his difficulties; but his conduct in the matter appears to have been much misrepresented. He was not, he declared, opposed to the plantation scheme; on the contrary, he warmly approved of it, only he objected to the way in which it was carried into execution. There was too much talk about it. The thing ought to have been done quietly and with celerity. Instead of that the Irish obtained wind of what was intended, and had time to band together, thereby not only obstructing the plantation, but considerably embarrassing him in the government. His views on the subject were undoubtedly sound, and were indeed recognised to be so by Essex himself, who, however much he might feel inclined to resent his unwillingness to co-operate and the alacrity with which he obeyed the order to disband, was obliged to admit that he had no other choice in the matter (Ham. Cal. 1572–5, passim;, Ireland, ch. xxix–xxxii.; , Lives of the Earls of Essex, vol. i.; , Monaghan).

The post of treasurer, which he resigned in 1573 to Sir Edward Fitton, far from being a lucrative appointment, had involved him in debts amounting to nearly 4,000l. The deputyship profited him nothing, and unless shortly relieved he declared he would be obliged to sell Milton; as it was, his wife had already been instructed to sell part of the stock on the property. At the last moment Elizabeth remitted 1,000l. and ‘stalled’ the rest, thus saving him from absolute beggary. These private difficulties, superadded to his bodily infirmities, rendered him extremely irritable, and led to one quarrel after another with Sir E. Fitton [q. v.] Despite his advice and that of Sir J. Perrot, the Earl of Desmond had in 1573 been allowed to return to Ireland, and though promptly rearrested in Dublin, he had a few months later managed to escape into Munster. Mischief was of course anticipated; but nothing was done—nothing indeed could be done so long as Fitton proved insubordinate. The queen was enraged, declaring that her honour was wounded so long as the traitor was allowed to continue abroad (Ham. Cal. ii. 15; Cal. Carew MSS. i. 464, 466, 473). Fitzwilliam replied that he had neither men nor credit to enable him to take the field. Compelled at length to act, he in August 1574 marched into Munster, captured in rapid succession Derinlaur Castle, Castlemagne, and Ballymartyr, and obliged the earl to submit himself at Cork on 2 Sept. For this service he had Elizabeth's thanks (Cal. Carew, i. 483), but he still continued