Already struggling with dwindling attendance and student truancy, the outbreak of the Northwest Resistance caused the school to be abandoned and brought a number of challenges for the principal, Rev. Thomas Clarke. After instruction was stopped at the school in 1885, the building was used as military barracks for Canadian troops fighting the resistance movement.Students of the school were scattered by the resistance, some of whom went missing. At the end of March the townspeople fortified themselves in the Mounted Police barracks. The school was initially plundered by the townspeople and the police before they fortified themselves in the barracks. Members of the rebellion also looted some of the abandoned homes in the area and the school's food supplies. Later in the summer the school started to be used to station Canadian troops. In autumn of 1885 the principal was notified that the school would be needed as winter barracks for a gunnery battery. The Northwest Resistance brought with it a host of problems for the school. Even after the facilities had been renovated and were back in use, the school struggled to increase enrolment to the revised expectations of thirty boys and thirty girls. Rev. Thomas Clarke was defended the school and his staff against accusations of mistreatment including poor diet and lack of medical treatment. He also was accused of keeping children longer than agreed upon and of not allowing parents to remove their children from the school whenever they desired.
(T. Clarke, Sessional Papers, 1887, Paper 6, p.140) (MacDonald Papers, vol. 290, L.Vankoughnet to MacDonald, 15 October, 1885) (Clarke Papers, file 103, diary entries of 10-11 Sept. and and 15 and 30 Oct. 1885.)