Deterministic models have long been used to model the individual effectiveness of elements of the Ballistic Missile Defense System (BMDS). Agent-based models (ABMs) emphasize the specification of the individual components comprising a system and demonstrate higher order system properties through the interactions of those components. ABMs are particularly suited to (1) complex systems where it is easier to understand or observe the individual components rather than the dynamics that govern their interactions and (2) systems where empirical data is insufficient to provide statistical representations. New missions and capabilities desired by national leadership call for increased interaction between the BMDS elements and their subsystems. New capabilities and mission threads include launch on remote and engage on remote capabilities as well as a robust missile defense system capable of defending against threat raids, debris, and decoys. These new capabilities and mission threads may require modifications to kill chains and command and control constructs as well as improved coordination and performance. These capabilities must be realized through modifications to programs of record and integration across elements of the system that have their own independent programmatic momentum. A robust missile defense system must be achieved through a construct of layered defenses. Change in capabilities requires analysis of the complex interdependencies between Standard Missile (SM-3), SPY, and BMDS elements such as PATRIOT, Terminal High-Altitude Area Defense, Aegis Ashore Missile Defense System, etc. Synergy among the systems (termed “elements”) is required to meet the new challenges, which can be accomplished through systems of systems engineering. Definition and testing of the interactions between the systems are crucial to provide situational awareness via analysis of data transfer between the elements. ABMs are a tool that allows qualitative evaluation of these interactions of the complex BMDS. This paper presents an investigation of agent-based modeling as a method to explore the system interrelationships and evaluate the indeterminacy of the BMDS kill chain.