Background: Exposure to trauma and potentially morally injurious events may lead to moral injury (MI). The link between MI and posttraumatic stress disorder (PTSD) may have particularly relevant implications for treatment-resistant PTSD (TR-PTSD). Multi-modal Motion-Assisted Memory Desensitization and Reconsolidation (3MDR), a technology-assisted exposure-based trauma therapy that has been used in the treatment of PTSD, may also be an acceptable modality for patients in the treatment of TR-PTSD and MI. This proof-of-concept study aimed to investigate (1) whether MI co-occurs in military members (MMs) and veterans with TR-PTSD, and (2) the perspectives of MMs and veterans with TR-PTSD utilizing 3MDR for MI. Methods: This study employed a mixed-methods clinical trial. Military Members and veterans participated in this study (N = 11) through self-reported questionnaires, video recordings of treatment sessions, and semi-structured interviews post-session and post-intervention, with longitudinal follow-up to 6 months. Results: MI scores correlated with self-reported measures of mental health symptoms related to PTSD. The thematic analysis revealed three emergent themes: (1) Realities of War, (2) Wrestling Scruples, and (3) Moral Sensemaking. Conclusion: MI was highly correlated with TR-PTSD and themes regarding MI. This result, while preliminary, allows for the postulation that MI may be contributing to the continuation of PTSD symptoms in TR-PTSD, and that 3MDR may be an acceptable modality for addressing these symptoms in MMs and veterans.