In April 1921, Aiken's IRA unit took a Protestant church congregation hostage in Creggan, County Armagh in order to ambush the Police and Special Constabulary arriving for the service. One Special was killed in ensuing ambush. Although Aiken then released the Protestant civilians unharmed, the incident heightened local sectarian animosity. Starting the following month, the Special Constabulary started shooting Catholic civilians in revenge for IRA attacks.In June 1921, Aiken organised his most successful attack on the British military, when his men detonated a mine under a British troop train headed from Belfast to Dublin, killing the train guard, three cavalry soldiers and 63 of their horses. Shortly afterwards, the Specials took four Catholics from their homes in Bessbrook and Altnaveigh and killed them.
The cycle of violence continued in the area in the following year, despite a formal truce with the British as of 11 July 1921. Michael Collins organised a clandestine guerrilla offensive against the newly created entity of Northern Ireland in May 1922. For reasons that have never been properly determined, Aiken and his Fourth Northern Division never took part in the operation, although it was planned that they would. Nevertheless, the local IRA's inaction at this time did not end the bloodshed in South Armagh. Aiken has been accused by unionists of ethnic cleansing of Protestants from parts of South Armagh, Newry, and other parts of the north, in particular the killing of seven Protestant civilians in Altnaveigh in June 1922. The incident was a revenge attack for the killing the previous day of two local Catholics and the sexual assault of a woman by the Special Constabulary.
The IRA split over the Anglo-Irish Treaty of 1921 and this left Aiken ultimately aligned with the Anti-Treaty side in the Irish Civil War in spite of personal efforts to prevent division and civil war. Aiken tried to remain neutral and after fighting broke out between pro and anti treaty units in Dublin, he wrote to Richard Mulcahy, calling for a truce and the removal of the Oath of Allegiance (Ireland) from the Free State constitution. He took no part in the fighting until he was arrested, along with over 300 of his men, who were billeted in Dundalk by the Free State Army on 14 July. However, just ten days later he was freed in a raid on Dundalk prison. Then, on 14 August, he led a surprise attack of 300–400 anti-treaty IRA men on Dundalk. They blew holes in the army barracks there and rapidly took control of the town at a cost of just two of his men killed. The operation freed 240 republican prisoners and seized 400 rifles. However, while in possession of the town, Aiken publicly called for an end to the civil war. For the remainder of the conflict, Aiken and his unit remained at large, carrying out some guerrilla attacks on Free State forces; however, Aiken was never enthusiastic about the internecine struggle.
He succeeded Liam Lynch as IRA Chief of Staff in March 1923, and issued the cease fire and dump arms orders on 24 May 1923, that effectively ended the Irish Civil War. He remained Chief of Staff of the IRA until 12 November 1925
Aiken was first elected to Dáil Éireann as a Sinn Féin candidate for Louth in 1923, continuing to be re-elected for Fianna Fáil at every election until his retirement from politics fifty years later. He entered the first Fianna Fáil government as Minister for Defence, later becoming Minister for the Co-ordination of Defensive Measures with responsibility for overseeing Ireland’s national defence and neutral position during the Second World War (see The Emergency).
McNeill took offence at de Valera's response and against government advice, published his correspondence with de Valera. De Valera then formally advised King George V to dismiss the Governor-General. The King arranged a special deal between both men, whereby McNeill would retire from his post a few weeks earlier than planned, with the resignation coinciding with the dates de Valera had suggested for the dismissal.
Though the governor-generalship of the Irish Free State was controversial, the media and even anti-governor-generalship politicians in the opposition Labour Party publicly, and even members of de Valera's cabinet privately, criticised Aiken and O'Kelly for their treatment of McNeill, who all sides saw as a decent and honourable man. Aiken refused to discuss the affair later in life. De Valera later made amends by appointing Mrs McNeill as an Irish ambassador.
Aiken was Minister for Finance for three years following the war and was involved in economic post–war development, in the industrial, agricultural, educational and other spheres. However, it was his two periods as Minister for External Affairs that Aiken fulfilled his enormous political potential. As Foreign Minister he adopted where possible an independent stance for Ireland at the United Nations and other international forums such as the Council of Europe. Despite a great deal of opposition, both at home and abroad, he stubbornly asserted the right of smaller UN member countries to discuss the representation of communist China at the General Assembly. Unable to bring the issue of the partition of Ireland to the UN (because of Britain's veto on the Security Council) and because of unwillingness of other Western nations to interfere in what these Western nations saw as British affairs at that time (the US taking a more ambiguous position), Aiken ensured that Ireland vigorously defended the rights of small nations such as Tibet and Hungary, nations whose problems he felt Ireland could identify with and had a moral obligation to help.
Aiken also supported the right of countries such as Algeria to self-determination and spoke out against apartheid in South Africa. Under Ireland’s policy of promoting the primacy of international law and reducing global tension at the height of the Cold War, Aiken promoted the idea of areas of law, which he believed would free the most tense regions around the world from the threat of nuclear war.
He also introduced the so-called 'Aiken Plan' to the United Nations in an effort to combine disarmament and peace in the Middle East, Ireland a country being on good terms with both Israel and many Arab countries. In the UN the Irish delegation sat between Iraq and Israel and formed a kind of physical 'buffer' and in the days of Aiken (who as a minister spent a lot of time with the UN delegation) both the Italians (who on their turn sat in the vicinity of the Iraqi delegation), the Irish and the Israeli claimed to be the one and only UN-delegation of New York, a city inhabited by many Irish, Jewish and Italians.
Aiken was also a champion of nuclear non-proliferation and he received the honour of being the first minister to sign the Nuclear Non-Proliferation Treaty in 1968 in Moscow.
Aiken's impact as Minister for External Affairs was such that he is sometimes seen as the father of Irish foreign policy. His performance was praised in particular by a later Minister for Foreign Affairs, Fine Gael's Garret FitzGerald, himself a later holder of the office.
They contrasted his continuing bitterness towards Blythe with the cross party friendships of their colleagues Seán MacEntee (anti-treaty) and Desmond FitzGerald (pro-treaty) who after the divide re-established relationships and ensured their children held no civil war bitterness. Great rivals Éamon de Valera and W. T. Cosgrave, after years of enmity, also became reconciled in the 1960s. However Aiken refused to reconcile with former friends who had taken sides in the Civil War.
Frank Aiken died on 18 May 1983 in Dublin from natural causes at the age of 85. He was buried with full State honours in his native Camlough, County Armagh, Northern Ireland.
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