On 28 June, Free State forces arrested his party, including Deasy, but Free State general Eoin O'Duffy allowed them to leave the city. Later it was stopped by a Free State patrol in County Kilkenny and spent some time with enemy officers. A Free State publication stated that Lynch had been released on the understanding that he disavowed the approach of the 'Irregulars'. O'Duffy was adamant that Lynch had assured him that he would not take up arms against the government. For his part, Lynch issued a vehement denial of any such undertaking having been given, in which regard he was supported by
Florrie O'Donoghue and Deasy. Lynch now began organising resistance elsewhere. On 1 July 1922 IRA forces occupied portions of Limerick city. At this time Lynch also sent a note to the leader of the Free State forces to discuss the possibility of a truce. Lynch wished to establish a "
Munster Republic", which he believed would frustrate the creation of the Free State. This "Munster Republic" would be defended by the "Waterford-Limerick Line". From south-east to north-west, this consisted of the city of
Waterford, the towns of
Carrick-on-Suir,
Clonmel,
Fethard,
Cashel,
Golden, and
Tipperary, and ended at the city of
Limerick, where Lynch established his headquarters. He led Limerick's defence, but it fell to Free State troops on 20 July 1922. He retreated further south and set up his new headquarters at Fermoy. The "Munster Republic" collapsed in August, when Free State troops
landed by sea in Cork and Kerry. Cork City was taken on 8 August and Lynch abandoned Fermoy on 11 August 1922. The Anti-Treaty forces then dispersed and
pursued guerrilla tactics. His counterpart Michael Collins was killed in an ambush at
Béal na mBláth, Cork on 22 August, a week after the death of
Arthur Griffith. Lynch contributed to the growing bitterness of the war by issuing what were known as the "orders of frightfulness" against the Provisional Government on 30 November 1922. This general order sanctioned the killing of Free State
TDs (members of parliament) and senators, as well as certain judges and newspaper editors, in reprisal for the Free State's
killing of captured republicans. The first republican prisoners to be put to death were four captured IRA men on 14 November 1922, followed by the execution of republican leader
Erskine Childers on 17 November. These orders were acted upon by IRA men, who killed TD
Seán Hales and wounded another TD outside the Dáil on 7 December 1922. In response, the Free State shot four republican leaders,
Rory O'Connor,
Liam Mellows,
Dick Barrett and Joe McKelvey the next day. This led to a cycle of atrocities on both sides, including the Free State official execution of 77 republican prisoners and "unofficial" killing of roughly 150 other captured republicans. In early February 1923 Lynch issued a notice that the IRA would begin reprisals if the executions of prisoners continued. Lynch's men, for their part, launched a concerted campaign against the homes of Free State members of parliament. Among the acts they carried out were the burning of the house of TD
Seán McGarry, resulting in the death of his seven-year-old son, the murder of Free State minister
Kevin O'Higgins' elderly father and the burning of the O'Higgins' family homestead at
Stradbally in early 1923. Lynch wrote to
Éamon de Valera that "Free State supporters are traitors and deserve the latter's stark fate". Lynch was heavily criticised by some republicans, notably O'Malley, for his failure to coordinate their war effort and for letting the conflict peter out into inconclusive and defensive guerrilla warfare. Other IRA volunteers felt that while Lynch was a decent man, he had failed to organise and lead the anti-treaty forces properly and did not possess the mind-set of a revolutionary to strike early for a swift victory. Lynch was scathing of the Dáil and the old IRA GHQ for having abandoned the people in the North, "particularly in Belfast" (see
The Troubles in Ulster (1920–1922)). In March 1923, the Anti-Treaty IRA Army Executive met in a remote location in the Nire Valley. Several members of the executive proposed ending the civil war; however, Lynch opposed them and narrowly carried a 6–5 vote to continue the war. He had been trying to import mountain artillery from Germany in a vain attempt to turn the tide of the war. When killed, he was carrying documents that appeared to call for the end of the war. ==Death==