The efficient deployment of weapons in military operations is critical for mission success, and the flow of air within the weapon bay of an autonomous fighter drone plays a vital role in achieving this objective. In this paper, we present a comprehensive numerical simulation and computational fluid dynamics (CFD) analysis of the three-dimensional lid-driven cavity flow within the weapon bay of an autonomous fighter drone. To address this challenging problem, we employ CFD analysis and a multigrid approach to solve the Navier-Stokes equations for the aerodynamic problem. Our simulations include high Reynolds numbers of up to 10,000, which demonstrates the potential of CFD analysis in optimizing the design of autonomous fighter drones for military operations. We evaluate the effectiveness of the linked strongly implicit multigrid technique in estimating high-Re fine-mesh flow solutions using the vorticity-stream function formulation of the two-dimensional incompressible Navier-Stokes equations. The model issue is the driven flow in a square cavity, and we consider meshes up to 1024 x 1024 points and combinations with Reynolds numbers as high as 1000. To further improve the accuracy of our simulations, we employ one-dimensional grid clustering coordinate transformations instead of uniform mesh refinement, as the flow field exhibits one or more secondary vortices. Our findings demonstrate that CFD analysis can provide valuable insights into the complex flow dynamics within the weapon bay of autonomous fighter drones, which can lead to the optimization of their design for enhanced mission capabilities. Overall, our study highlights the significance of numerical simulations and CFD analysis in the design and optimization of autonomous fighter drones for military applications. Our results can serve as a basis for future research in the field of UAV aerodynamics and contribute to the development of more efficient and effective military operations.