Indonesia’s frontier, outermost, and underdeveloped islands face multidimensional challenges involving geographical isolation, limited public services, socioeconomic disparities, maritime security risks, and uneven institutional capacity, requiring collaborative approaches to strengthen national resilience. This study examined the implementation of Indonesian Navy cooperation with civilian institutions, local governments, and communities in enhancing sustainable resilience across strategically significant island regions. A mixed-methods multiple-case study integrated quantitative assessments, semi-structured interviews, field observations, document analysis, and cross-case comparisons to evaluate cooperation quality, collaborative implementation, community capacity, institutional integration, and resilience outcomes. The findings revealed that effective cooperation strengthened maritime awareness, institutional coordination, community preparedness, public-service accessibility, and adaptive capacity when programs incorporated clear institutional roles, integrated resources, local participation, and implementation continuity. Community capacity and institutional integration emerged as critical mechanisms linking strategic maritime cooperation with multidimensional island resilience. The study concludes that institutional presence and short-term assistance alone do not automatically strengthen national resilience. Sustainable cooperation requires local ownership, strengthened civilian institutions, durable collaborative networks, and community self-reliance. Indonesian Navy cooperation contributes most effectively when its maritime reach, logistical capabilities, and organizational capacity complement civilian governance while enabling island communities to develop sustainable capacities for managing security, socioeconomic, environmental, and connectivity-related challenges independently.