In this research, a wide-body aircraft was analyzed with critical monitoring of its states, a function of several control inputs (wind gust, turbulence, and microburst). The aerodynamic and stability coefficients of a Boeing 747-200 were obtained from previously published works and 6- DOF equations were formulated. Simulations were conducted for various control inputs to determine the aircraft’s free response, as well as the forced response. In order to understand the nature of the atmosphere, three different models were incorporated, including (i) the Dryden Model, (ii) wind gust, and (iii) microburst. The aircraft was found to be stable in the longitudinal and lateral flight modes, with trim conditions agreeing with published data. For a vertical wind gust of −10 ft/s, the AoA and pitch rate were observed to oscillate sinusoidally and became stable with new trim conditions. These states were found to regain trim conditions once the gust was removed. In the case of 3D gust, it was found that the longitudinal modes achieved a new trim condition through Phugoid oscillations, whereas the lateral modes underwent short-period oscillations. For the case of turbulence, random fluctuations were observed for trim conditions with no unstable behavior. When considering the microburst case, it was found that the aircraft initially gained altitude in the region of the headwind; this was followed by a sharp descent under the influence of a vertical velocity component.