While the electorate had indicated overwhelming approval for the treaty, the prospects for the Provisional Government were not so appealing at the onset of the war, as the anti-treaty IRA, or Irregulars as they would be increasingly labeled, held the loyalty of many units throughout the country. However, the government was able to assert its control over Bublin in the first two weeks, capturing significant anti-treaty leaders such as O'Connor and Mellows. Cathal Brugha was fatally wounded when he refused to surrender. Harry Boland also was wounded, captured, and died in prison. 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. However, the government received two severe blows in August. On August 12 Arthur Griffith, the founder of Sinn Fein and the president of the nominal Bail fiireann, died of a cerebral hemorrhage. Ten days later, Michael Collins, who had placed the civilian direction of the government in the hands of William T. Cosgrave for the duration of the war while he directed the military operations as commander in chief, was killed in an ambush at Beal na blath, County Cork, not many miles from his birthplace.
Cosgrave became head of the Provisional Government. Significant figures in his government, which was approved by the third Dail fiireann (the parliament elected in June finally met on September 9), included Kevin O'Higgins, who was vice president and minister for home affairs (later Justice), Ernest Blythe, Desmond FitzGerald, Richard Mulcahy, Joseph McGrath, Patrick Hogan, Fionan Lynch, and Eoin MacNeill. For the most part, the leading figures, with the exception of Mulcahy, were men involved in the civilian rather than the military phase of the struggle, and they would come to regard the treaty as a sacred bond, rather than a tactical concession that could be scrapped should the occasion and the prospects of achieving full republican status permit. Collins, some suggest, was not as temperamentally disposed to the role of constitutionalist.
Because there was no legal basis on which the Provisional Government could arrest and try irregulars, other than British martial law proclamations, the government asked for and received Bail passage of a resolution calling for an emergency system of military courts with powers of trial, imprisonment, and execution. It could only be a resolution since the constitution of the Free State had not yet been approved and the Bail did not yet have possess powers. The government's position was further strengthened on October 10 when the Catholic hierarchy of Ireland condemned the violent resistance to the government.
Besides the military campaign against the Irregulars, the government attended to the passage of the constitution of the Irish Free State. The constitution was to be governed by the clauses in the treaty that were restrictive of Irish sovereignty, such as the role of a governor general to summon parliaments and sign legislation, the oath to the king, and so forth. The type of government was to be a parliamentary democracy, elected by STV proportional representation, with stipulated human rights of life, liberty, property, and due process. It included certain then fashionable experiments, such as the initiative and the referendum, and external ministers who were selected and would retain their positions independent of the cabinet. The constitution did not include radical concepts regarding social entitlements, women's rights, or restrictions on war powers advocated by some members, especially those from the Labour Party. The Bail approved the constitution on October 25. On December 5, legislation adopted by the Westminster parliament approved both the Free State Constitution and the Anglo-Irish Treaty of a year before, satisfying the British insistence that the Free State be based on constitutionalism and legislation rather than violence.
The very day the Irish Free State came into being, December 6, two members of its legislature were shot, one of whom was killed by the Irregulars as part of a retaliatory policy for the military court executions that had started a few weeks earlier in accord with the September 25 Bail resolution. Before the end of the war those courts would execute 77 people, more than had been executed by British military courts during the war of independence, and among the earlier victims was a leading anti-treaty figure, Robert Erskine Childers. In response to a threat by the republicans to attack any member of the Dail that had supported the emergency resolution, the Free State cabinet consented to the military's request to take immediate retaliatory action against four prisoners arrested months before at the Four Courts. Even the pro-government press and the archbishop of Dublin condemned the government's action, to which its vice president, Kevin O'Higgins, was the last to concur. One of those executed, Rory O'Connor, had a year before been best man at O'Higgins's wedding. However, there were no further assassination attempts on members of the Bail, although violence continued, including the burning of the homes of members of the upper house of the legislature, the Seanad, and the killing of O'Higgins's father, a physician in County Laois.
The Seanad, which had delaying powers over legislation, was elected by the lower house, except for a quarter of its members who were nominated by the government. It was designed to give a voice to the unionist and Protestant minority within the 26 counties of the Free State, whose participation was regarded as essential for the successful development of the new state, especially since many of them had played so significant a role in the economy and society of pre-independent Ireland.
For the first four months of 1923, the war consisted primarily of a mopping-up operation by the government. There were substantial casualties and atrocities committed by both sides. The government's employment of hardened Dublin revolutionaries, especially men who had worked under Michael Collins, in the actions in County Kerry met considerable rebuke, even from within the government. However, Mulcahy, the minister for defense, who had to rapidly construct a national army out of a mixture of loyal IRA members, former members of the British army, and raw recruits, understandably defended those under his command.
On April 10 Liam Lynch, the military commander of the irregulars, was killed in action. By April 27 de Valera, president of the revolutionary government that was formed to legitimize the Irregulars, called for the suspension of offensive operations and, a month later, after the government refused to consider suggestions for a treaty with the Irregulars, directed his followers to lay down their arms, ending the civil war. The war had cost hundreds of lives and thousands of casualties, not to mention millions of pounds damage to an economy that was desperately in need of capital for development. The peace began with more than 10,000 prisoners interned, whose acceptance of the legitimacy of the Free State and proclivity to return to violence was still uncertain.