Designing integrating systems for support, real-time monitoring, and executing of complex missions is challenging, since they often fail due to high levels of complexity and overwhelming volume of input data. Past attempts have resorted to “ad hoc” solutions, which face issues of being non-updatable, non-upgradable, and not applicable to similar missions, necessitating a complete redesign and reconstruction of the system. In the national defense and security sector, the impact of this reconstruction requirement leads to significant costs and delays. This study presents advanced methodologies for organizing large-scale datasets and handling complex operational procedures systematically, enhancing the capabilities of Decision Support Systems (DSSs). By introducing Complex Mission Support Systems (CMSSs), a novel SS sub-component, improved accuracy and effectiveness are achieved. The CMSS includes mission conceptualization, analysis, real-time monitoring, control dynamics, execution strategies, and simulations. These methods significantly aid engineers in developing DSSs that are highly user-friendly and operational, thanks to human-reasoning-centered design, increasing performance and efficiency. In summary, the systematic development of data cores that support complex processes creates an adaptable and adjustable framework in a wide range of diverse missions. This approach significantly enhances the overall sustainability and robustness of an integrated system.