In 1641 a major rebellion broke out in Ireland, led by northern Catholics such as Sir Phelim O'Neill and Lord Maguire. While continuing to pledge allegiance to Charles I, they launched attacks on Protestant inhabitants. While much of Ulster and Connaught was seized, an attempt to capture Dublin failed. O'Farrell was one of many exiled officers who returned to join the army of the rebels, who established their own government in Kilkenny.