Systems-Theoretic Process Analysis (STPA) helps mitigate identified safety hazards leading to unfortunate situations. Usually, a systematic step-by-step approach is followed by safety experts irrespective of any software based tool-support, but identified hazards should be associated with security risks and human factors issues. In this paper, a design framework using Integrating Requirements and Information Security (IRIS) and open source Computer Aided Integration of Requirements and Information Security (CAIRIS) tool-support is used to facilitate the application of STPA. Our design framework lays the foundation for resolving safety, security and human factors issues for critical infrastructures. We have illustrated this approach with a case study based on real life Cambrian Coast Line Railway incident.