As Riel's religious pronouncements became increasingly heretical the clergy distanced themselves, and father Alexis André cautioned Riel against mixing religion and politics. Also, in response to bribes by territorial lieutenant-governor and Indian commissioner Edgar Dewdney, local English-language newspapers adopted an editorial stance critical of Riel. Nevertheless, the work continued, and on 16 December Riel forwarded the committee's petition to the government, along with the suggestion that delegates be sent to Ottawa to engage in direct negotiation. Receipt of the petition was acknowledged by Joseph-Adolphe Chapleau, Macdonald's Secretary of State, although Macdonald himself would later deny having ever seen it. By then many original followers had left; only 250 remained at Batoche when it fell in May 1885.
While Riel awaited news from Ottawa he considered returning to Montana, but had by February resolved to stay. Without a productive course of action, Riel began to engage in obsessive prayer, and was experiencing a significant relapse of his mental agitations. This led to a deterioration in his relationship with the Catholic hierarchy, as he publicly espoused an increasingly heretical doctrine. On 11 February 1885, a response to the petition was received. The government proposed to take a census of the North-West Territories, and to form a commission to investigate grievances. This angered a faction of the Métis who saw it as a mere delaying tactic; they favoured taking up arms at once.
Knowing that he could not defeat the Canadians in direct confrontation, Dumont had hoped to force the Canadians to negotiate by engaging in a long-drawn out campaign of guerrilla warfare; Dumont realised a modest success along these lines at the Battle of Fish Creek on 24 April 1885. Riel, however, insisted on concentrating forces at Batoche to defend his "city of God". The outcome of the ensuing Battle of Batoche which took place from 9 to 12 May was never in doubt, and on 15 May a disheveled Riel surrendered to Canadian forces. Although Big Bear's forces managed to hold out until the Battle of Loon Lake on 3 June, the rebellion was a dismal failure for Métis and Natives alike, as they surrendered or fled.
Several individuals closely tied to the government requested that the trial be held in Winnipeg in July 1885. Some historians contend that the trial was moved to Regina because of concerns with the possibility of an ethnically mixed and sympathetic jury. Tom Flanagan states that an amendment of the North-West Territories Act (which dropped the provision that trials with crimes punishable by death should be tried in Manitoba) meant that the trial could be convened within the North-West Territories and did not have to be held in Winnipeg.
Prime Minister Sir John A. Macdonald ordered the trial to be convened in Regina, where Riel was tried before a jury of six English and Scottish Protestants, all from the area surrounding the city. The trial began on 28 July 1885, and lasted five days. Riel delivered two long speeches during his trial, defending his own actions and affirming the rights of the Métis people. He rejected his lawyer's attempt to argue that he was not guilty by reason of insanity, asserting,
Before his execution, Riel was reconciled with the Catholic Church, and assigned Father André as his spiritual advisor. He was also given writing materials so that he could employ his time in prison to write a book. Louis Riel was hanged for treason on 16 November 1885 at the North-West Mounted Police barracks in Regina.