This document presents the underlying theory for an unsteady computational model of the transient aerothermodynamics of a deformable vehicle entering an atmosphere at hypersonic speeds. Many unique features of the problem require unusual computational capabilities. The large accelerations associated with the vehicle's flight dynamics results in the body-fixed reference frame being non-inertial, and the governing equations must be modified to include this effect. The vehicle's structural deformations and ablation requires the inclusion of the effects of a moving solid boundary, with a nonuniform mass flux across that boundary. A computational chemistry capability must be included to treat the thermochemical nonequilibrium of the high-temperature gas dynamics, and the reactions between the ablation products and the dissociated air. The theory required to treat these phenomena are described in this report.