He served as the Public Health Agency of Canada's (PHAC) vice president of logistics and operations from November 27, 2020 to May 14, 2021, leading the federal government's COVID-19 vaccine rollout, but was removed from that role after the Canadian Forces National Investigation Service initiated an investigation into him following an allegation of sexual assault between January 1 and April 30, 1988 [5][6] while he was a student at Royal Military College Saint-Jean.

From 2015–2017 he was assigned as Deputy Commanding General (Operations) for I Corps of the United States Army[8] in Joint Base Lewis-McChord near Tacoma, Washington.

Fortin then served as director of operations in the foreign and defence policy secretariat at Canada's Privy Council Office (2017–2018), and subsequently was appointed Commander 1st Canadian Division based in Kingston, Ontario.

[16] In his ruling, Judge Richard Meredith concluded the complainant was sincere in her belief that she was assaulted but noted several significant inconsistencies with her testimony, citing numerous factors that could easily have led to mistaken identity on the night in question.

[17] In a statement to media post-ruling, Fortin reiterated his innocence and claimed from the start, senior military and political decision-makers presumed and acted as if he was guilty – thereby denying him due process, and mishandling as well as leaking information about his case.

"[19] On June 14, 2021, Fortin filed a request for judicial review of the decision to remove him from his PHAC role, seeking either reinstatement or assignment to another position suitable for his rank.

On January 23, 2023, an internal review led by Vice-Admiral Bob Auchterlonie concluded that on the balance of probabilities Fortin did not engage in sexual misconduct, so no further administrative measures were required.

[24] On October 18, 2023, media reported that several senior military and civilian leaders in National Defence claimed they had "no records" relating to Fortin when asked under Access to Information and Privacy legislation.

[27] On April 20, 2023, the MPCC agreed to conduct a public interest investigation, citing in part, months of delay by the military's provost marshal office in providing full disclosure of the case file to the oversight body.