A firm believer in collective leadership, Mr Lynch saw his role as Taoiseach essentially as chairman of the Government. He strenuously sought to reconcile the rival factions within Fianna Fail during the early part of his tenure in office. He also sought to continue the new dialogue initiated by Mr Lemass with the Northern Prime Minister, Captain Terence O'Neill.
His own position as leader was strengthened by a series of successful by-elections, including one in May, 1968, when Desmond O'Malley retained the seat of his late uncle Donagh for the party in East Limerick. Mr O'Malley was to become a protege of Mr Lynch, who publicly acknowledged him as a future potential leader.
An attempt by Mr Lynch's administration later that year to scrap proportional representation was, however, roundly defeated, but this did not stop the party winning the general election of June, 1969, comparatively comfortably.
In January, 1969, when the civil rights campaign was beginning to degenerate into violence, Mr Lynch made it clear at the party ardfheis in Dublin that his policy would be one of non-violent intervention in the North. He told the party faithful that "the first aim of Fianna Fail today is to secure by agreement the unification of the national territory". He made a further plea for practical patriotism rather than sabre-rattling speeches in April, but there was a growing demand within the party for the assertion of more traditional republican values. The most vocal exponent of this position was Mr Blaney. But at least two other senior Ministers, Mr Kevin Boland and Mr Haughey, held similar views.
When fighting erupted in Derry after the Apprentice Boy's march of August 12th, a clear split emerged at the emergency Cabinet meeting that followed. Some Ministers demanded that troops be sent into Derry and Newry to protect the Catholic minority. Mr Lynch took a firm stand against intervention, arguing that even if it was desirable, it was impracticable because of the Army's state of unreadiness. After protracted debate, he pulled the Cabinet with him by a narrow majority in what was undoubtedly the single most important political act of his career.
That night he went on RTE to warn the British government that his own could "no longer stand by and see innocent people injured and perhaps worse. It is obvious that the RUC is no longer accepted as an impartial police force. Neither would the employment of British troops be acceptable nor would they be likely to restore peaceful conditions - certainly not in the long term."
Mr Lynch announced that military field hospitals would be set up on the Border to help refugees, and local defence and FCA units were mobilised as well. It was part-gesture to his own irredentist militants, part-support for the beleaguered Catholics in the North and part-insurance that paramilitaries from the South did not intervene across the Border.
Nevertheless, Mr Lynch's speech, corrupted in the popular mind to read "we will not stand idly by", became a taunt for long afterwards from Northern militants, especially in the Provisional IRA, who also nicknamed him " `Union Jack' Lynch".
In an effort to provide practical help and maintain a common front within Fianna Fail, a Northern subcommittee of the Cabinet was set up and the Dail voted a special £100,000 relief fund for distress in Northern Ireland. The breach within the Cabinet continued to grow, however, with Mr Colley and Dr P. J. Hillery, the future President and EEC Commissioner, most vocal in their opposition to the hawks. Mr Lynch continued to assert that "the Border cannot be changed by force" (in his response to the Downing Street declaration that promised limited internal reforms in the North) but added that "to continue to ignore the need for constitutional change, so clearly necessary, could only have a tragic result".
At the Fianna Fail Ard Fheis in January, 1970, Mr Lynch warned his internal critics as much as the British, unionists and paramilitaries, that "until the ugly blooms of mistrust and suspicion which poison the atmosphere have died and the ground is planted with fresh, clean seeds of friendship and mutual confidence, reunification can never be more than an artificial plant rather than a burgeoning blossoming flower."
Through the coming months, however, there were increasing rumours that some members of the Cabinet subcommittee on the North were exceeding their brief and on May 6th Mr Haughey, Minister for Finance, and Mr Blaney, Minister for Agriculture, were sacked from the Cabinet, while Mr Boland, Minister for Local Government, resigned in protest.
Two days earlier the Minister for Justice, Mr Micheal O Morain, had also resigned. All were casualties of the Arms Crisis, an attempt to import weapons paid for with Government funds to arm the Northern nationalists. In a protracted series of two trials which lasted until October 23rd, Mr Haughey and other defendants in the case were acquitted.
With the loss of so many senior Ministers over such a short period, many observers felt an election was inevitable, but Mr Lynch displayed a cool shrewdness in reshuffling his Cabinet and serving out most of his term after winning a crucial Dail vote of confidence a week after the Ministerial sackings. He also successfully resisted attempts by Mr Boland and others to call an emergency ardfheis.
Mr Lynch correctly read the underlying desire for a united front within the party and the desire for stability among the people at large. Nevertheless, it was perhaps inevitable that a split had occurred within Fianna Fail which would continue to rack it for the next decade or more.
While the drama of the Arms Crisis overshadowed Mr Lynch's second Government, there were many other major developments. The most significant was the EEC referendum, following negotiations with the existing members of the Community in which Mr Lynch and his Minister for Foreign Affairs, Dr Hillery, played the leading roles. Mr Lynch himself had talks with all the EEC leaders, including a crucial visit to President de Gaulle, who had been vetoing British membership of the EEC and, thereby, Irish membership.
The electorate voted five to one in favour of the terms. Dr Hillery, who had been a firm Lynch supporter in the Northern controversy, became Ireland's first EEC Commissioner, losing the Taoiseach a valued ally in Cabinet. During the year Mr Lynch consolidated his position by winning a by-election in Cork, where Gene Fitzgerald was elected.
Mr Lynch's first Government had a number of modest achievements to its credit, including the establishment of the Labour Court and other modern industrial relations structures through the 1969 Industrial Relations Act.
The only event to incur personal criticism on the Taoiseach himself was his decision to accept a round-the-world tour on Gulf Oil's new supertanker, Universe Ireland, after its new storage depot at Bantry Bay was opened.
Other achievements during Mr Lynch's second term of office included the restructuring of the health service on more efficient lines through the 1970 Health Act, an expansion of the diplomatic service and development of redundancy legislation initiated by Mr Lemass.
But 1972 was the difficult year, with the Northern crisis producing its highest death toll for any 12-month period. This included the civil rights marchers gunned down by British paratroopers in Derry on Bloody Sunday, and the burning of the British Embassy in Dublin by angry demonstrators in retaliation. The Irish ambassador was temporarily withdrawn from London. The Northern crisis continued to generate fears in the Republic of an over-spill of the violence and the Lynch administration had no difficulty passing emergency legislation strengthening the Offences Against the State Act.
With the North very much in mind, the Government also held a referendum to delete Article 44 of the Constitution, which had recognised the special position of the Catholic Church in the Republic. The Catholic Hierarchy was among the wide range of interest groups welcoming the change. The voting age of the electorate was lowered to 18 in a second referendum.
In February, 1973, Mr Lynch felt confident enough that he had quelled dissidents within the party and vindicated his stand on the Northern crisis with the public to call an early election.
To the surprise of many, Fine Gael and Labour hammered out a coalition programme which concentrated on domestic issues such as rising levels of inflation, unemployment and taxation. The Government was defeated, although Mr Lynch topped the poll in his native Cork and the party had actually increased its share of the vote from 45.7 per cent in 1969 to 46.2 per cent.