The great Irish rebellion began on 23 October 1641, and in December Inchiquin accompanied the president in an expedition against the Leinster rebels who were harassing Waterford and Tipperary. All the prisoners taken in a fight near Carrick-on-Suir were executed by martial law. In April 1642, during the siege of Cork by Viscount Muskerry with four thousand men, Inchiquin, "one of the young and noble-spirited commanders," led a sally of two troops of horse and three hundred musketeers, which broke up the Irish camp for a time. Muskerry left baggage and provisions behind, and Inchiquin was able to ship guns and to take two castles on the west side of Cork harbour which had annoyed the navigation. St. Leger died on 2 July, and Inchiquin became the legal governor of Munster, as he announced to the lords justices before the end of the month. David Barry, 1st Earl of Barrymore, was associated with him in the civil government but died on Michaelmas day. Alexander Forbes, 11th Lord Forbes, with Hugh Peters as his chaplain, landed at Kinsale early in July with forces provided by adventurers in England; but he paid no attention to Inchiquin's request for help, and he effected nothing. On 20 August Inchiquin, accompanied by Barrymore, Viscount Boyle of Kinalmeaky, and Roger Boyle, Lord Broghill, with only two thousand foot and four hundred horse, overthrew General Garret Barry at Battle of Liscarrol with seven thousand foot and fifteen hundred horse; but he lacked means to improve his victory, though seven hundred are said to have fallen on one side and only twelve on the other. He was himself wounded in the head and hand.