Increasingly agile manoeuvre is an advantage in the flight of aircraft, missiles and aerial vehicles, but the principles of accelerating aerodynamics in the transonic regime are only now being fully investigated. This study contributes to the understanding of shock and separation effects on drag during axial acceleration, using a simple geometric configuration. Unsteady shock wave behavior was numerically investigated for an axisymmetric cone-cylinder using a commercial solver and the Moving Reference Frame acceleration technique. This acceleration technique was validated using unsteady numerical and experimental methods. The cone-cylinder was accelerated from Mach number 0.6 to Mach number 1.2 at 100g constant and deceleration was from Mach number 1.2 until Mach number 0.6 at –100g constant. Three cone angles were tested for the cone-cylinder with uniform cylinder diameter. Acceleration through the transonic Mach regime was characterised by a delayed and gradual shock wave development when compared to steady state, demonstrating a clear flow history effect. Deceleration through the transonic Mach regime was characterised by shock wave propagation from the base to the nose. New flow structures appeared during deceleration that do not have counterparts in the steady state, including shock interactions and propagating expansion-compression features. Gross changes in the unsteady drag coefficient curves for each cone-angle are explained with reference to unsteady shock wave behaviour for accelerating and decelerating motion.