This thesis continues to develop a conceptual methodology for the design of a warship that is capable of showing how naval architecture related decisions interact with operational measures of effectiveness through the use of modeling and simulation. Beginning with a brief overview of recent developments in total ship design approaches, it supports an overarching method that directly supports capability-based decisions. Using a simple medium-tonnage patrol vessel and a Maritime Intercept Operation (MIO) mission in a fictional setting, operational and ship design synthesis models are developed. Critical design criteria (responses) in each model are measured using relevant design variables (factors) based on mission measures of performance used in creating experimental designs. The resulting models are then linked, both mathematically and using graphs, to show how decisions made by the naval architect can directly influence a single operational measure of effectiveness. Decision makers can then assess various system outcomes by trading off performance parameters to make capabilitybased decisions.