Multi-agent cyber-physical systems (CPSs) are ubiquitous in modern infrastructure systems, including the future smart grid, transportation networks, and public health systems. Security of these systems are critical for normal operation of our society. In this paper, we focus on physical layer resilient control of these systems subject to cyber attacks and malicious behaviors of physical agents. We establish a cross-layer system model for the investigation of cross-layer coupling and performance interdependencies for CPSs. In addition, we study a two system synchronization problem in which one is a malicious agent who intends to mislead the entire system behavior through physical layer interactions. Feedback Nash equilibrium is used as the solution concept for the distributed control in the multi-agent system environment. We corroborate our results with numerical examples, which show the performance interdependencies between two CPSs through cyber and physical interactions.