(D'Ewes, Diary in Harl. MS. 164, f. 167). Neither Conyers nor Astley would hear of that plan, and meanwhile the secret committee of the House of Commons had reported on the first plot. On 14 June O'Neill was summoned to answer for his share in it, but fled from York, and, in spite of his reported capture in Norfolk, escaped to Brussels in safety.
A committee of the house was appointed to inquire into his proceedings, and in August his pay was stopped ; in September O'Neill returned to Wey bridge with Sir John Berkeley, and surrendered himself at Pym's house in Chelsea during the recess. Alter an examination bail was refused, and he was taken into custody by the sergeant-at-arms. On 20 Oct. he was committed to the gatehouse, and on 4 Dec. was brought to the bar of the house. He pleaded the act of oblivion, but this was disallowed ; it was resolved to impeach him, and articles of high treason were passed on 13 Dec. After further examination by the House of Lords, his trial was Postponed by a difference between the two houses ; in January 1642 he was removed, on the plea of ill-health, to the Tower, whence on 6 May he escaped in female attire, and made his way to Brussels in spite of proclamations for his arrest (Treason Discovered, or the Impeachment of Daniel Oneale, 1641 ; Oneale's Escape out of the Tower, 1642 ; Commons' Journals, ii. 175, &c. ; Lords' Journals, iv. 399, &c. ; Evelyn, Diary, ed. Bray, App. passim).
On the outbreak of the civil war O'Neill returned to England; his first commission was that of major in Colonel Osborne's regiment (Masson, Life of Milton, ii. 442 ; Peacock, Army Lists, p. 17) ; in October he was with Rupert at Abingdon, complaining of the bad discipline of his troops (Warburton, Prince Rupert, ii. 82). His promotion was retarded by Charles I, who could not forgive O'Neill's hostility to Strafford. In June 1643 he was lighting at Gloucester, and on 27 Sept. was at the first battle of Newbury. During the winter he was at Oxford (Carte, Original Letters, &c. i. 26). In January 1643-4 he was selected to accompany Randal MacDonnell, second earl of Antrim [q. v.], on his mission to Ormonde, with the object of procuring ten thousand Irish troops for England and three thousand for Scotland. O'Neill was on good terms with Ormonde, and had great influence over Antrim, with whom he was distantly connected. By a court intrigue of Digby's, detailed at great length by Clarendon, O'Neill was previous to his departure made groom of the bedchamber by Charles, under the impression that it would be long before he returned to assume his duties. He arrived at Kilkenny on 23 Feb., and superintended the despatch of fifteen hundred troops for Scotland, but otherwise the mission was unsuccessful. O'Neill had returned to Beaumaris by 25 June, and joined Rupert's army in time to take part in the battle of Marston Moor on 2 July; he commanded Rupert's regiment of foot (Sanford, Studies of the Great Rebellion, p. 595 ; Markham, Life of Fairfax, pp. 161-9). He then joined the army of the west, at Bath, on 17 July, and marched into Devonshire 'Essex-hunting' (O'Neill to Trevor in Carte, Original Letters, i. 58-61); he was present in September when Essex allowed nimself to be surrounded in Cornwall, and fought at the second battle of Newbury on 27 Oct. He was again at Oxford during the winter, and fought at Naseby on 14 June 1645; he was then directed, on 27 June, to proceed to Falmouth to procure ships, probably in order to secure a retreat for Prince Charles (Husband, A Collection of Ordinances, 1646, pp. 855-6 ; Ludlow, Memoirs, ed. 1753, iii. 306). Thence he was sent with a letter of recommendation from Charles I to Ormonde, and landed at Passage, co. Waterford, on 24 Aug.
For the next few years O'Neill was principally engaged in fruitless negotiations between his uncle Owen Roe and Ormoude, and in endeavours to save the royalist cause in Ireland. In 1647 he was treating with Sir James Turner and the Scots (Turner, Memoirs, Bannatyne Club, p. 47); and in October of the same year he was despatched by Ormonde to seek aid at St. Germains, when he took part, as second, in the duel between Digby and Wilmot (O'Neill to Ormonde in Carte, Original Letters, i. 146-59). Returning to Ireland, he was made governor of Ormonde's horse-guards, and served with Castlehaven in Carlow (Castlehaven, Memoirs, ed. 1753, pp. 87, &c.) In July 1649, as governor of Trim, he defended that town against the parliamentarians, and in the autumn he brought to a successful issue the fresh negotiations with Owen Roe, which had been started early in the year. Soon after he was sent with two thousand foot and four hundred horse to recover places in Down and Antrim, but retired on finding the country completely in the power of the parliamentarians. O'Neill was now promoted major-general, a step which subsequently formed one of the charges brought by the bishops against Ormonde (Cox, Hibernia Angl. vol. ii.) For a short time during his uncle's illness he actually commanded the Ulster army, being the only man from whom