System architecture analyses of distributed ship systems offer a practical view of system behavior over all operational states; however, the effectiveness of these analyses can be bound by limited computational performance or capability. Deactivation diagrams provide an alternative view to conventional system architecture descriptions, allowing for rapid analysis of system connectivity and flow based on precomputed single-state system descriptions. This thesis explores the development of system deactivation diagrams and their use in early-stage naval ship system design. Software tools developed in C++ and VBA as part of this research support the Virginia Tech (VT) Naval Ship Design Concept and Requirements Exploration (CandRE) process and tools utilizing the U.S. Navy's Leading-Edge Architecture for Prototyping Systems (LEAPS) framework database. These tools incorporate automated path-finding algorithms developed based on proven network theory and effective computational methods for use in performing ship system deactivation analysis. Data drawn from the results of this approach possess extensible applicability towards studies in naval ship system vulnerability, flow optimization, network architecture, and other system analyses. Supplementary work on interfacing the LEAPS framework libraries with deactivation analyses has demonstrated the capability for generating deactivation diagrams from complex LEAPS ship system databases and paved the way for future incorporation of LEAPS into research work at Virginia Tech.