While many organizations claim to "put safety first," safety is rarely considered early in the design process when system-level architectural decisions are made. Instead, system design follows an abstraction-to-detail process to first meet functional and then performance requirements. Following this process, safety assurance occurs in the later stages of design through a rigorous expert review process. The significant cost of safety-based redesign and the growing complexity of engineered systems motivates a need for early design-stage fault analysis. This research presents a novel method of including safety into the model-based design and analysis of complex systems using low-fidelity behavior simulations. Specifically, this research demonstrates the adaption of the functional design process to explicitly include the system property of safety in the system representation. Next, early design fault analysis is extended to connect component failure behavior to system-level hazards. Finally, this research develops three methods of results clustering to provide different evaluation metrics of the system design. In summary, this research demonstrates a framework for incorporating safety into early design decision making. This research addresses safety and failure in the design of complex systems incorporating diverse technology domains as found in energy, transportation, and aerospace systems.