A Unified Debugger that enables the debugging of graphical models with combinations of entities from multiple domains such as time-based block diagrams, statecharts, and physical system models, with additional features for the debugging of hand-written and automatically generated code is disclosed. A view of the entity being executed that is consistent with the type of the modeling domain to which the entity currently being executed belongs is automatically generated for a user. Rather than requiring a user to manually transition from one debugger to the next, the Unified Debugger applies the appropriate debugging features from each modeling domain. The Unified Debugger also enables integration of diagnostic information from a multitude of modeling domains into a central user interface. In addition, a standard diagnostic interface which spans a plurality of modeling domains is defined that enables the customization of debug behavior.