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Confederation of Canada, 1864–1867

As his government had fallen again, Macdonald approached the new governor general, Lord Monck, to dissolve the legislature. Before Macdonald could act on this, Brown approached him through intermediaries; the Grit leader believed that the crisis gave the parties the opportunity to join together for constitutional reform. Brown had led a parliamentary committee on confederation among the British North American colonies, which had reported back just before the Taché-Macdonald government fell. Brown was more interested in representation by population; Macdonald's priority was a federation that the other colonies could join. The two compromised and agreed that the new government would support the "federative principle" – a conveniently elastic phrase. The discussions were not public knowledge and Macdonald stunned the Assembly by announcing that the dissolution was being postponed because of progress in negotiations with Brown – the two men were not only political rivals, but were known to hate each other.

The parties resolved their differences, joining in the Great Coalition, with only the Parti rouge of Canada East, led by Jean-Baptiste-Éric Dorion, remaining apart. A conference, called by the Colonial Office, was scheduled for 1 September 1864, in Charlottetown, Prince Edward Island; the Maritimes were to consider a union. The Canadians obtained permission to send a delegation – led by Macdonald, Cartier, and Brown – to what became known as the Charlottetown Conference. At its conclusion, the Maritime delegations expressed a willingness to join a confederation if the details could be successfully negotiated.

In October 1864, delegates for Confederation met in Quebec City for the Quebec Conference, where they agreed to the Seventy-Two Resolutions, the basis of Canada's government. The Great Coalition was endangered by Taché's 1865 death; Lord Monck asked Macdonald to become premier, but Brown felt that he had as good a claim on the position as his coalition partner. The disagreement was resolved by appointing another compromise candidate to serve as titular premier, Narcisse-Fortunat Belleau.

In 1865, after lengthy debates, Canada's legislative assembly approved confederation by 91 votes to 33. None of the Maritimes, however, had approved the plan. In 1866, Macdonald and his colleagues financed pro-confederation candidates in the New Brunswick general election, resulting in a pro-confederation assembly. Shortly after the election, Nova Scotia 's premier, Charles Tupper, pushed a pro-confederation resolution through that colony's legislature. A final conference, to be held in London, was needed before the British Parliament could formalise the union. Maritime delegates left for London in July 1866, but Macdonald, who was drinking heavily again, did not leave until November, angering the Maritimers. In December 1866, Macdonald both led the London Conference, winning acclaim for his handling of the discussions, and courted and married his second wife, Agnes Bernard. Bernard was the sister of Macdonald's private secretary, Hewitt Bernard; the couple first met in Quebec in 1860, but Macdonald had seen and admired her as early as 1856. In January 1867, while still in London, he was seriously burned in his hotel room when his candle set fire to the chair he had fallen asleep in, but Macdonald refused to miss any sessions of the conference. In February, he married Agnes at St George's, Hanover Square. On 8 March, the British North America Act, 1867, which would thereafter serve as the major part of Canada's constitution, passed the House of Commons (it had previously passed the House of Lords). Queen Victoria gave the bill Royal Assent on 29 March 1867.

Macdonald had favoured the union coming into force on 15 July, fearing that the preparations would not be completed any earlier. The British favoured an earlier date and, on 22 May, it was announced that Canada would come into existence on 1 July. Lord Monck appointed Macdonald as the new nation's first prime minister. With the birth of the new nation, Canada East and Canada West became separate provinces, known as Quebec and Ontario, respectively. Macdonald was appointed a Knight Commander of the Order of the Bath (KCB) on that first observance of what came to be known as Dominion Day, later called Canada Day, on 1 July 1867.