The War Office recalled Nugent to supervise the raising of the 85th Buckinghamshire Volunteers in March 1794. He commanded the regiment under Sir Ralph Abercromby in the action at Fort St. Andries, and with Major General David Dundas at Tuil on the river Waal and participated in the disastrous retreat from the Rhine. Promoted to major general on 1 May 1796, he became Captain of St Mawes Castle on 5 November 1796 and served in that role until his death. He went on to be commander of the northern district of Ireland in 1798, in which post he played an important part in placating the people of Belfast during the Irish Rebellion that year, and became Adjutant-General in Ireland in August 1799. He also represented Charleville, County Cork in the last Irish House of Commons before the Acts of Union 1800.