his command in the English army (Carte, iii. 324; Bellings, iv. 19; Old Parliamentary History, xvi. 83).
In the summer of 1647, when parliament and the army quarrelled, Waller followed the lead of Cromwell, was one of the officers appointed to negotiate with the commissioners of the parliament, and helped to draw up the different manifestoes published by the army (Clarke Papers, i. 110, 148, 217, 279, 363). He took no great part in the debates of the army council, but his few speeches show good sense, moderation, and a desire to conciliate (ib. i. 339, 344, ii. 87, 103, 180). When the second civil war broke out Waller's regiment was quartered at Exeter, and, though there were some local disturbances, he had no serious fighting to do (Lords' Journals, x. 269; Rushworth, vii. 1130, 1218, 1306). In December 1648 Waller acted as Colonel Pride's chief coadjutor in the seizure and exclusion of presbyterian members of parliament, and personally laid hands on Prynne (Old Parliamentary History, xviii. 448; Walker, History of Independency, ii. 30). He was appointed one of the king's judges, signed the death-warrant, and was absent from only one meeting of the high court of justice (Nalson, Trial of Charles I). In the reconquest of Ireland he took a prominent part, following Cromwell thither with his regiment in December 1649. As major-general of the foot, he commanded in the siege of Carlow in July 1650, took part in the two sieges of Limerick in 1650 and 1651, laid waste the barony of Burren and other places in the Irish quarters, and assisted Ludlow in the subjugation of Kerry (Ludlow, Memoirs, ed. 1894, i. 275, 302, 320; Gilbert, Aphorismical Discovery, iii. 180, 218, 310, 324). When resistance ended he was actively engaged in the settlement of the country and the transplantation of the Irish to Connaught (Prendergast, Cromwellian Settlement, pp. 123, 160, 270). The Long parliament granted him as a reward some lands he rented from the Marquis of Ormonde, and voted him an estate of the value of 1,200l. a year (Commons' Journals, vi. 433, vii. 270; Tanner MSS. liii. 139).
Waller supported the elevation of Cromwell to the protectorate, and was the only important officer present at his proclamation in Dublin (Ludlow, i. 375). He received, however, no preferment from Cromwell, and it was not till June 1657 that lands in the county of Limerick were settled upon him in fulfilment of the parliament's promise (Commons' Journals, vii. 492, 516, 553). Ludlow represents him as jealous of Lord Broghill, and intriguing to prevent his return to Ireland (Memoirs, ii. 5). Henry Cromwell, on the other hand, thought Waller hardly used, and warmly recommended him to Thurloe and the Protector. ‘I have observed him,’ he wrote to the latter, ‘to bear your highnesses pleasure so evenly, that I am more moved with that his quiet and decent carriage than I could by any clamour or importunity to give him this recommendation’ (Thurloe, iv. 672, vi. 773). On the fall of Richard Cromwell, Waller hastened to make his peace with the parliament by getting possession of Dublin Castle for them, and by writing a long letter to express his affection for the good old cause (Ludlow, Memoirs, ii. 101, 122). Yet he was not trusted, and Ludlow, when he was called to England in October 1659, left the government of the army to Colonel John Jones Waller justified this mistrust by refusing, ostensibly in the interests of the parliament, to let Ludlow land in Ireland at the end of December 1659 (ib. ii. 123, 147, 449). His conduct at this period was extremely ambiguous, and evidently inspired only by the desire to preserve himself. When Monck recalled the secluded members he became alarmed, and endeavoured to stop the movement, but was besieged in Dublin Castle by Sir Charles Coote, and delivered up by his own troops (ib. pp. 186, 199, 229). Coote imprisoned him for a time in the castle of Athlone, but Sir William Waller (1597?–1668) [q. v.] obtained permission for him to come to England, and the council gave him his freedom on an engagement to live quietly (ib. p. 239).
An impeachment had been drawn up against him by the officers of the Irish army for promoting the cause of Fleetwood and Lambert and opposing a free parliament, but it was not proceeded with; and Monck, though distrusting him as too favourable to the fanatics, had no animosity against him (Trinity College, Dublin, MS. F. 3, 18, p. 759; Warner, Epistolary Curiosities, 1st ser. p. 55). But as a regicide the Restoration made Waller's punishment inevitable. He escaped to France; but on the publication of the proclamation for the surrender of the regicides, he returned to England and gave himself up. At his trial, on 10 Oct. 1660, he at first refused to plead, but finally confessed the indictment. On 16 Oct., when sentence was delivered, he professed his penitence, adding that if he had sought to defend himself he could have made it evident that he ‘did appear more to preserve the king upon trial and sentence than any other’ (Trial of the Regicides, ed. 1660, pp. 17, 272). His petition for pardon is among the
