During the Irish War of Independence (1919-1921), he was appointed a Staff Captain in IRA General Headquarters (GHQ) and was involved in intelligence work, raids and the defence of nationalist areas in Belfast.
[1] Cooney was arrested by British forces in November 1920 and held in Ballykinlar Internment Camp, County Down until 8 December 1921.
Moving to Dublin in March 1922, he transferred to K Company, 1 Battalion, Dublin Brigade, IRA and used his position in the Grocers’ Assistants Union to give the IRA access to the union's Banba Hall, Parnell Square.
Taking the anti-Treaty side in the Irish Civil War, Cooney took part in the occupation and defence of several buildings around Parnell Square and Bolton Street against National forces.
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