O'Neill's later years were marked by infighting amongst the Confederates, and in 1647 he led his army to seize power in the capital of Kilkenny. His troops clashed with rival forces of the Confederacy, leading to O'Neill forming a temporary alliance with Charles Coote's English Parliamentary forces in Ulster. He initially rejected a treaty of alliance between the Confederates and the Irish Royalists, but faced with the Cromwellian invasion he changed his mind. Shortly after agreeing an alliance with the Lord Lieutenant of Ireland Ormond, in which he was promised an Earldom, he died on Tuesday, 6 November 1649.