This paper documents an integration of engine, plume, and computational fluid dynamics (CFD) analyses in the conceptual design of low-boom supersonic aircraft, using a variable fidelity approach. In particular, the Numerical Propulsion Simulation System (NPSS) is used for propulsion system cycle analysis and nacelle outer mold line definition, and a low-fidelity plume model is developed for plume shape prediction based on NPSS engine data and nacelle geometry. This model provides a capability for the conceptual design of low-boom supersonic aircraft that accounts for plume effects. Then a newly developed process for automated CFD analysis is presented for CFD-based plume and boom analyses of the conceptual geometry. Five test cases are used to demonstrate the integrated engine, plume, and CFD analysis process based on a variable fidelity approach, as well as the feasibility of the automated CFD plume and boom analysis capability.