In this study we examine the simulated downward transport and mixing of stratospheric air into the upper tropical troposphere as observed on a research flight during the SCOUT-O3 campaign in connection with a deep convective system. We use the Advanced Research Weather and Research Forecasting (WRF-ARW) model with a horizontal resolution of 333 m to examine this downward transport. The simulation reproduces the deep convective system, its timing and overshooting altitudes reasonably well compared to radar and aircraft observations. Passive tracers initialised at pre-storm times indicate the downward transport of air from the stratosphere to the upper troposphere as well as upward transport from the boundary layer into the cloud anvils and overshooting tops. For example, a passive ozone tracer (i.e. a tracer not undergoing chemical processing) shows an enhancement in the upper troposphere of up to about 30 ppbv locally in the cloud, while the in situ measurements show an increase of 50 ppbv. However, the passive carbon monoxide tracer exhibits an increase, while the observations show a decrease of about 10 ppbv, indicative of an erroneous model representation of the transport processes in the tropical tropopause layer. Furthermore, it could point to insufficient entrainment and detrainment in the model. The simulation shows a general moistening of air in the lower stratosphere, but it also exhibits local dehydration features. Here we use the model to explain the processes causing the transport and also expose areas of inconsistencies between the model and observations.