Identifying and assessing risk is one of the most important processes in managing complex systems and requires careful consideration. The need for an effective, efficient approach to risk management is considerably more important for defense projects based on systems of systems (SoS), because they are exposed to risk already in early stages of development. This paper uses advanced data science tools to present the complexity of the risk factors relevant to defense systems, and proposes a methodology for identifying, analyzing and monitoring the risks that they face. Findings from an in-depth analysis of 46 classified defense projects based on SoS shows a need to focus on three main risks faced by defense projects: uncertainty, the lack of clearly defined goals, and managing a system under constrained conditions. The paper also presents some recommendations for minimizing risk factors in SoS for defense projects.