Under the terms of the Anglo-Irish Treaty, the Treaty had to be ratified by popular vote and the Second Dáil had decided that the 16 June 1922 general election, campaigned on the Treaty, would be that ratification. By April, there were increasing clashes between government troops and irregulars and, in late April, Lynch attended public rallies with Michael Collins in Killarney and Tralee to argue for the Treaty, despite significant harassment from anti-treaty activists. Sinn Féin knew that the June election would split the party and in an effort to retain unity a Pact was drawn up in May 1922 under which it was agreed that both Pro and Anti-Treaty TDs would form a coalition government. The outcome of June 1922 election was strongly in favour of acceptance of the Treaty, both in the number of Pro-Treaty TDs elected and the votes cast. However, there were continuing disagreements about the Anglo-Irish Treaty, combined with many acts of aggression against treaty supporters as well as National Forces leading ultimately to the civil war, with the shelling of the Four Courts on 28 June 1922 being a significant watershed moment. During the
Civil War he fought with the
Irish National Army and rose to the rank of Brigadier-General. He enlisted in the National Army at
Portobello Barracks on 12 July 1922, as a General Staff Officer in the General Headquarters Staff. By mid-summer the major cities were under government control and the Irregulars were concentrated in the rural areas of the province of Munster, particularly in the counties of Tipperary, Cork, and Kerry. In July 1922, with the sub-division of the original military districts, Lynch was appointed by Collins a vice commandant of the South Western Division with the rank of commandant-general, commanding a unit of Dublin soldiers in County Kerry. He served in that appointment under General
Eoin O'Duffy, General Officer Commanding the Division, up to 13 December 1922. He undertook trips to his constituency in Kerry and the rest of the county but the population of the county was heavily anti treaty and there was considerable danger. On occasion he had to endure being ambushed and, during one ambush, he was hit on a metal cigarette case which saved his life. In August 1922, he travelled by car with Michael Collins as far as Limerick, where Lynch headed for his constituency of Kerry and Collins for Cork, but on 22 August 1922 Collins was ambushed and assassinated. On Friday, 25 August 1922, Lynch, in command of a large force of Dublin Guards, set out for
Kenmare to relieve and strengthen the garrison that had been established earlier in the month by Tom O’Connor-Scarteen. The geography meant that the Kenmare could only be supplied by sea and a land link was necessary. As Lynch's column advanced along the Killarney-
Kilgarvan road it came under fire from anti-treaty forces at Filadown, near
Glenflesk. This brought an ironic comment to Lynch, TD for the area, that his constituents did not seem to think much of him. As night fell, and following a number of wounded, the Free State column retreated, returning to the area the next day. He was elected to the
3rd Dáil at the
1922 general election as a
Pro-Treaty Sinn Féin TD and on 9 September 1922, Lynch was appointed as a
Minister without Portfolio in the government of the Third Dáil, being unavailable for immediate service in the Government as he remained on active service. On 6 December 1922, the day the Irish Free State came into being, two members of its legislature were shot by the Irregulars, one of whom,
Seán Hales, was killed, as part of a retaliatory policy for the military court executions that had started a few weeks earlier. Following the execution of the Four Courts IRA members, a threat was published that all pro-treaty TDs were legitimate targets for assassination. However, the reluctance of former colleagues to attack him may have ensured his survival during the war – Frank Henderson of Dublin's No. 1 brigade of the IRA told Ernie O'Malley of his reluctance to become involved in reprisal shootings after Free State executions, commenting: ‘I didn't like that order. I could have shot Eamon Duggan and Fionán Lynch, for they went home every night drunk, but I left them alone.’ Although the civil war ended in 1923, Lynch was provided with an armed guard as late as 1932, because of the ongoing threat of assassination. ==Later life==