MacCarthy was at Cork to welcome James on his arrival, and was left in command there when the king hurried to Dublin. He followed him later with the forces raised in Munster, and was made master-general of artillery in Mountjoy's place. He hesitated about accepting the post, though it was made specially independent of the English master-general, lest it should injure his prospects in France, but Avaux reassured him on that point (D'Alton). He disarmed the protestants throughout Cork, and had the whole county at his mercy (cf. Smith, bk. iii. ch. vii.) In the parliament which met on 7 May MacCarthy sat as member for the county which he had thus reduced, and brought up to the lords the bill for the repeal of the Act of Settlement. On the following day, 24 May (3 June) 1689, he was created Viscount Mountcashel.
The new peer was very soon sent with some of the best available troops against Enniskillen. On 28 July news came to the latter town that MacCarthy was attacking Crom Castle, at the south end of Lough Erne, and on the 31st the Enniskilleners, under Wolseley, won the decisive battle of Newtown Butler. Londonderry was relieved on the same day. The Irish writers say the two armies at Newtown Butler were about equal, 3,500 in each. According to Macaulay and the authorities whom he followed, MacCarthy had great numerical superiority; and perhaps it is not now possible to discriminate exactly. The defeated general sought death in a skirmish which followed the main battle, but was recognised and spared, the victors being glad to mark their sense of the humanity which he had shown in saving Colonel Crichton from the ferocious Galmoy. He told his captors ‘that he found now the kingdom like to be lost, his army being the best (for their number) that King James had, unless those before Derry, who were then much broken, and that he came with a design to lose his life, and was sorry that he missed of his end, being unwilling to outlive that day’ (Macariæ Excidium, note 102).
MacCarthy was kindly treated at Enniskillen, and allowed the freedom of the place on parole. He escaped by bribing a sergeant named Acheson, who was hanged for his share in the business. Schomberg exclaimed that he took Lieutenant-general MacCarthy to be a man of honour, but would not expect that in an Irishman any more. The account most favourable to him is that he announced an intention to break his parole, that Governor Hamilton placed him, in consequence, under a guard, and that he assumed this to be a cancelling of his parole. He was acquitted by a court-martial in France in the following year, but the evidence against him could scarcely be heard there, and the defence cannot be considered satisfactory (Irish Brigades, p. 51; Macariæ Excidium, note 103). Shrewsbury believed him a man of honour, whose word was to be relied on, but this testimony was given before his escape from Enniskillen.
MacCarthy reached Dublin in December 1689, and was afterwards chosen to command the Irish regiments which Louis XIV demanded in exchange for those sent to Ireland under Lauzun. He had been a thorn in Tyrconnel's side, who is supposed to have favoured the selection in order to get rid of a troublesome opponent. The parole difficulty may have contributed to this result. MacCarthy's regiment had been cut to pieces at Newtown Butler, but he easily recruited it again. The ships which brought Lauzun and his men returned with the Irish brigade, and reached Brest at the beginning of May. Dangeau says 5,800 Irishmen landed. Their leader was colonel of the first of the three regiments into which they were divided. He made good terms for himself and his men. Each private received a sol a day more than the French rate of pay, and MacCarthy himself had a sol a day for every man in the brigade under him (Irish Brigades, p. 18). He was made a French lieutenant-general, with a pension of four thousand crowns, and Louis also gave him four thousand crowns for his outfit. He was soon sent to serve under St. Ruth in Savoy, and distinguished himself greatly in the action near Moutiers-de-Tarentaise on the night of 11 Sept. 1690. He received a wound in the breast, which at the time was thought slight, but which was afterwards believed to have caused his death (MacGeoghegan, iii. 749). After this he was left in command at Chambery with three thousand Irish. In June 1691 he was sent to serve under the Duke of Noailles in Catalonia, and was present at the capture of Urgel. The arrival in France of the Irish army, which followed Sarsfield after the capture of Limerick in October 1691, did not much change MacCarthy's position. He continued to command his original brigade of three regiments, and served on the Rhine under Marshal de Lorges in 1693. He died 1 July 1694 at the baths of Barèges, ‘of wounds,’ says the ‘Gazette de France,’ ‘received on several occasions, in all of which he distinguished himself extremely’ (Irish Brigades, i. 281). We are told that he was short-sighted, and that this lessened his military usefulness. Swift's tripos skit, written in 1688, men-