In the present work we study the dynamics of a supersonic missile canopy, separated in-flight. We distinguish between three separation phases: rotation about a fixed hinge, canopy-missile reciprocity, and free-canopy flight regime. The complementary numerical investigation conducted is two-fold. First, a segregated scheme is considered where an aerodynamic model, embodying the different flight phases, is constructed and introduced into a tailored three degrees-of-freedom (3DOF) rigid-body simulation. The aerodynamic model, obtained by quasi-steady RANS computations, consists of various canopy positions and orientations at specified flight conditions, to facilitate high fidelity trajectories based on a lean and efficient dataset. Then, a coupled unsteady-flow and multi-body dynamics framework is considered, and the realized canopy trajectories are compared with those obtained by the segregated approach to a satisfying agreement. The suggested scheme is shown to be beneficial to the robust design of canopy separated configurations.