In this paper, we utilize a software engineering technique called statistical debugging to experimentally identify emergent behaviors in a System of Systems. We apply the technique to an agent-based model of the Ballistic Missile Defense System (BMDS) in which each component of the BMDS has operational and managerial independence as well as geographic distribution. We develop a simple game where the BMDS (blue) is attacked by enemy threats (red) and repeat the game for a large number of replications. Results show that there is no strategy that guarantees a blue win. In addition, there are more losing strategies than winning ones and finally there are four strategies that appear in half the wins and the losses. We refer to those as emergent, since they cannot be controlled by either the red or the blue side.