The NASA Atmospheric Effects of Aviation Project (AEAP) Global Modeling Initiative (GMI) three-dimensional (3-D) chemical transport model (CTM) was applied to assess the impact of a fleet of high-speed civil transports (HSCTs) on abundances of stratospheric ozone, total inorganic nitrogen (NOy), and H2O. This model is specifically designed to incorporate a diversity of approaches to chemical and physical processes related to the stratosphere in a single computing framework, facilitating the analysis of model component differences, modeling intercomparison and comparison with data. A proposed HSCT fleet scenario was adopted, in which the aircraft cruise in the lower stratosphere, emitting nitrogen oxides (NOx) and water (H2O). The model calculated an HSCT-induced change in Northern and Southern Hemisphere total column ozone of +0.2% and +0.05%, respectively. This change is the result of a balance between an increase in local ozone below approximately 25 km and a decrease above this altitude. When compared to available NOy observations, we find that the model consistently underestimates lower stratospheric NOy. This discrepancy is consistent with the model bias toward less negative ozone impact, when compared to results from other models. Additional analysis also indicates that for an HSCT assessment it is equally important for a model to accurately represent the lower stratospheric concentrations of ozone and H2O. The GMI model yields good agreement in comparisons to ozone data for present-day conditions, while H2O is constrained by climatology as much as possible; thus no further biases would be expected from these comparisons. Uncertainties due to discrepancies in the calculated age of air compared to that derived from measurements, and of the impact of emissions on heterogeneous and polar chemistry, are difficult to evaluate at this point.