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In March of 1870, three delegates left for Ottawa to negotiate the terms of entry into Confederation. The government was convinced to introduce the Manitoba Bill in the House of Commons. On May 12, 1870, the Manitoba Act, based on the Métis List of Rights, was passed by the Parliament of Canada. The Bill included provisions that protected Métis lands, guaranteed their right to religion and to the use of their language in the legislature and the courts. Riel, as head of the Provisional Government, was charged with maintaining peace and order while awaiting the arrival of the first Lieutenant-Governor, Adams G. Archibald, and the troops that would accompany him.
The troops, which arrived before Archibald, were supposed to restore order and keep the peace. But some of the soldiers were out to avenge the death of Thomas Scott. Warned of their intentions, Riel had time to flee to sanctuary in the United States.
Riel awaited news from Red River in the Métis settlement of St. Joseph in the Dakota Territory. He was encouraged to remain in hiding as his life would be in danger if he returned. The dispute between the Métis and the troops were growing in number and Riel found it difficult to remain in hiding. He returned in September and intervened in a plan for the Métis to join with the Irish Fenians in a raid on Manitoba. Believing that the Métis future lay with Canada, not with the United States, Riel assured Archibald that the Métis would not join the Fenians and he kept his word.
Although grateful for his support against the Fenians, Archibald determined that he would be able to better keep the peace if Riel left the country for a while. Riel reluctantly accepted a $1,000 payment and left Manitoba in February, 1872 with bounty hunters in pursuit. Again he found it difficult to stay away and Riel returned in June where be began to campaign as a candidate in the federal election for the Manitoba constituency of Provencher. On the advice of friends, he eventually withdrew in favour of George-Etienne Cartier, who had been defeated in his own riding. Riel believed that Cartier would defend the Métis cause. However, Cartier died a few months later and although Louis was subsequently elected by acclamation, the House would not allow him to take his seat. Frustrated, he returned to the United States. In May 1874, he tried for a second time to take his seat, but once again had to flee to New York.
In 1877, the new Prime Minster, Alexander Mackenzie, granted Riel amnesty for the trouble in 1869-1870 on the condition he not return to Canada for five years. Exile was a time of anguish for Louis. He was often depressed and claimed that he had visions of a mission to fulfil. His uncle, John Lee, eventually took him to Montreal where he was confined to an asylum under the name of Louis R. David. Shortly thereafter, he was transferred to the asylum at Beauport where he gradually recovered his health.