Deep reasoning procedures are model-based, inferring single or multiple causes and/or timing relations from the knowledge of behavior of component models and their causal structure. The overall goal of this paper is to develop an automated deep reasoning methodology that exploits deep knowledge of structure and behavior of a system. We have proceeded by building a software environment that uses such knowledge to reason from advanced symbolic simulation techniques introduced by Chi and Zeigler. Such reasoning system has been implemented and tested on several examples in the domain of performance evaluation, and event-based control.