In 1641 he placed himself in opposition to his powerful Anglican cousin - James, Earl (later the Duke) of Ormonde. At the commencement of hostilities in the Irish Rebellion of 1641, he appeared inclined to espouse the Government side, and was appointed joint Governor of Kilkenny with the earl. Fearing, however, that the rights and liberties of his Catholic brethren would be still further interfered with, he wrote an explanatory letter to the Earl and took possession of Kilkenny in the name of the Confederates. He endeavoured to protect the lives and property of the Protestants, without relaxing his efforts for the side he had espoused. He then detached parties to secure other adjacent towns, which was done with such success that in the space of a week all the fortresses in the counties of Kilkenny, Waterford, and Tipperary were in their power.