The Australian threat environment has changed as a result of global terrorism and foreign fighters, which are contributing factors to the blurring of the lines between military objectives and law enforcement activities. This shift requires a more integrated and interoperable forensic science framework that is coordinated at the whole-of-Government enterprise level. The forensic science ‘system of systems’ provides an integrating framework, which recognizes that forensic science supports the criminal justice, law enforcement, intelligence, and military systems. These systems must work together to achieve end-to-end performance, which is coordinated through integration and sharing of information across the systems. The purpose of this paper is to discuss why we need a systems thinking approach to military forensic science in the contemporary world. Implementation of a coordinated and interoperable military forensic science system of systems will contribute to the Australian Department of Defence strategic objective to deter, deny and defeat returned foreign fighters and global terrorist networks, such as Islamic State of Iraq and Syria (ISIS).