The earliest days of the COVID-19 pandemic in Canada were marked by a significant surge in COVID cases and COVID-related deaths among residents of long-term care facilities (LTCF). As part of Canada's response to the COVID-19 pandemic, Canadian Armed Forces (CAF) personnel were mobilized for an initial emergency domestic deployment to the hardest-hit LTCFs (Operation LASER LTCF) to support the remaining civilian staff in ensuring the continued delivery of care to residents. Akin to what was observed following past CAF international humanitarian missions, there was an expected increased risk of exposure to multiple stressors that may be psychologically traumatic and potentially morally injurious in nature (i.e., related to important values; e.g., witnessing human suffering). The objective of the research study is to identify and quantify the individual-, group-, and organizational-level risk and resilience factors associated with moral distress, moral injury and traditional mental health and well-being outcomes of Operation (Op) LASER LTCF CAF personnel. The objective of this manuscript is to document the methodology, implementation procedures, and participation metrics. A multimethod research initiative was conducted, consisting of two primary data collection studies (a quantitative survey and qualitative interviews). The quantitative arm was a complete enumeration survey with online self-report questionnaires administered at three timepoints (3, 6, and 12 months post-deployment). The qualitative arm consisted of individual interviews conducted virtually, with a focus on understanding the nuanced lived experiences of individuals taking part in the Op LASER LTCF deployment. CAF personnel deployed to Op LASER LTCF (n = 2,595) were invited to participate in the study. Data collection is now complete. Overall, 1,088, 582, and 497 individuals responded to the survey at Time 1 (3 months), Time 2 (6 months), and Time 3 (12 months) post-deployment, providing a participation rate of 41.9%, 22.4%, and 19.2% for Time 1, Time 2, and Time 3, respectively. Data for all three timepoints was obtained from 212 participants (representing 19.5% of all Time 1 responses). Interest in participating in qualitative interviews surpassed expectations with over 200 individuals expressing interest; this allowed for purposive sampling across key characteristics, including gender, rank, Op LASER LTCF role, and province. In total, 53 interviews were conducted. The data generated by this research has the potential to inform and better understand the well-being and mental health of Op LASER LTCF personnel over time, identify general and Op LASER LTCF-specific risk and protective factors, provide necessary supports to the military personnel who served in this mission, and to inform preparation and interventions for future missions, especially those more of a domestic and humanitarian nature. DERR1-10.2196/44299.