When Bowell took power after Thompson's sudden death, he was faced with the problem of the Manitoba School Act. Should the Federal Government intervene in the Provincial question and support denominational schools from the public purse.

Bowell had originally come from Suffolk, England and once he was in Canada he became a prominent member of the Orangemen which was a pro-protestant anti-Catholic group. From his base in Belleville he organized and ran as the Tory candidate under MacDonald and was elected to Parliament in 1867. He served as the Minister of Customs and then Abbott appointed him the Minister of the Militia.

Bowell was chosen by Lord Aberdeen, the Governor General, to form a Conservative Government. Bowell was neither qualified nor able to fill the role placed upon him. On January 29, 1895 the Manitoba schools question was decided in favour of the Federal Government and it was given the right to intervene and give the Catholic schools the support of the Government. Bowell felt that Laurier, the leader of the Liberal party would have to support his decision and pushed through the legislation which gave the Catholics their schools back. He faced a rebellion form not only his own party, but from his supports in the Conservative party who refused to accept this pro-catholic decision. Seven of his cabinet resigned over the issue and Bowell was forced into an unwinable position. A few weeks later he submitted his formal resignation and Charles Tupper replaced him. Bowell then returned to the Senate and sat in that chamber for 23 years more, always unable to forgive the party members who had rebelled and forced him from office.