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Modeling and simulation environments are needed to support decision making in Navy Warfighters, which are emergent systems that pose a challenge to operations management. Ships consist of complex interconnected systems such as the infrastructure, crew, and workflow. A system-of-systems approach using agent-based modeling is applied here to develop workflow simulations involving a ship's crew conducting routine maintenance, watch duty, and reporting functions. Simple models are used to describe basic behavioral traits and intelligence in crew members; machinery including sensors for intelligent maintenance; equipment consuming power; mobile and stationary communication network access points; models for data transfer over the network; crew mobility models; power distribution and trimming models for the electrical system; and a fire model to simulate emergency scenarios. The simulation results demonstrate an increase in machine availability due to the implementation of intelligent maintenance systems. The effects of wireless-network usage on crew resource utilization and overall ship capability in normal operational scenarios are also demonstrated. A simple rescheduling algorithm is used to improve crew utilization and estimate manning requirements. The effects of emergency scenarios such as fires in different locations are also studied. Sensitivity analysis is presented to verify the developed model, and a note on validation is given.