Although it is debatable to what extend Naval Vessels will have to comply with strict regulations concerning exhaust emissions, concerning fuel supply there is a unanimous consensus about the need for independence from countries in conflict areas. Alternative fuels might provide this independence along with a reduction of in radiated noise. In this paper a concept design of a Power, Propulsion and Energy System of a Surface Combatant with the focus on significant reduction of greenhouse gas emissions is composed and simulated. Following the MBSE approach a user needs analysis resulted in a logical and physical PPE system design, focusing on four different military mission types. The design is a combined solution of Dual Fuel Methanol Internal Combustion Engines and Fuel Cells that run on compressed hydrogen. It shows advantages in efficiency, emissions and radiated noise. It can run in different modes, including a Zero Emission mode. To verify the design a dynamic Simulink model of the PPE system was built and coupled with a model of the propeller and hull in MARIN’s XMF framework, which includes waves. A particular Test Case was performed for a highly dynamic military operation involving a turning circle at high speed, while repetitively firing a railgun. The simulation shows the PPE system is capable to deliver and control the required power, at the edge of stability of the implemented DC distribution system. Following the W-model, a future iteration of the virtual model cycle can further improve system behavior.