 Following the collapse of Emmett's rising, Cloney was again arrested and lodged in Dublin Castle and later in Kilmainham Gaol from where he was released on health grounds in November 1804.After his release, Cloney went to live at Graiguenamanagh, County Kilkenny, where his home was nicknamed "Whitehall".Of the principal leaders of the 1798 rebellion, he, along with Joseph Holt was only one of two rebel leaders to survive and remain in Ireland.