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Magan was interned in the Curragh during the Irish Emergency (during the Second World War). In March 1946, he was arrested along with a number of other IRA men in the Ardee Bar, Dublin. Jailed, he was released in December 1946 along with Micksie Conway. Both men resumed their attempts to reorganise the IRA.
A lifelong bachelor and County Meath farmer, Magan sold his farm and devoted all his time and money to the IRA. He was appointed IRA chief of staff by the IRA Army Executive at its convention in September 1948. The IRA had almost been destroyed in the 1940s and Magan immediately set out to reorganise the political and military wings of the Republican Movement, namely the IRA and Sinn Féin, along with Michael Traynor, Paddy McLogan, and Tomás Mac Curtain.
Magan was not a popular choice for the position and several members of his previous IRA Army Council were not impressed by him but did not oppose his nomination outright. Magan drew support chiefly from Dublin delegates, who felt that "the Army needed a steel core and that Magan could supply it".
Magan was a determined physical force traditionalist. According to J. Bowyer Bell, he "wanted to create a new Army, untarnished by the dissent and scandals of the previous decade", with "no shadow of a gangster gunman, no taint of communism, but a band of Volunteers solely dedicated to reuniting Ireland by physical force". Tim Pat Coogan describes him as "priest-like - who had given all his money, time and thought to the IRA, a deeply religious man of the old-guard school of Irish Catholicism [and] when he was again interned in the Curragh during the 1950s Border Campaign he organised a flourishing branch of the Legion of Mary".
At the 1950 Sinn Féin Ardfheis, Magan was elected honorary joint secretary of the party. Coogan recounts that Magan's Sinn Féin submitted key political and economic policies for review by friendly clergy, "to ensure that they contained nothing contrary to Catholic teaching". In May 1951, the IRA leadership established a Military Council to draft an overall plan for the Republican Movement as a whole. Its members were Magan (as Chief of Staff), Tomás Mac Curtáin (as chairman of the Army Council), Pádraig Mac Lógáin (as president of Sinn Féin and chairman of the IRA Army Executive), a former British army officer with World War II experience service who was an expert on guerrilla warfare, and one other person.
In 1953, Magan played a role in organising and carrying out the Felstead arms raid. Unlike Seán Mac Stiofáin, Cathal Goulding, and Manus Canning, later jailed for the raid, Magan evaded arrest and managed to return safely to Ireland.
Magan was chief of staff and the commencement of the IRA's Border Campaign, codenamed Operation Harvest, which began on 11 December 1956.
He resigned from the Republican Movement in 1962 in a dispute over the relationship between the IRA and Sinn Féin.
Magan, who lived at 45 Lower Dodder Road in Rathfarnham, Dublin, subsequently worked as a taxi driver. He died on 4 July 1981 at Meath Hospital. On 8 July 1981 he was buried in Mount Jerome Cemetery, Dublin. A lifelong bachelor, he was survived by his sisters, nieces and nephews.