Autonomous exploration of subterranean environments constitutes a major frontier for robotic systems, as underground settings present key challenges that can render robot autonomy hard to achieve. This problem has motivated the DARPA Subterranean Challenge, where teams of robots search for objects of interest in various underground environments. In response, we present the CERBERUS system-of-systems, as a unified strategy for subterranean exploration using legged and flying robots. Our proposed approach relies on ANYmal quadraped as primary robots, exploiting their endurance and ability to traverse challenging terrain. For aerial robots, we use both conventional and collision-tolerant multirotors to explore spaces too narrow or otherwise unreachable by ground systems. Anticipating degraded sensing conditions, we developed a complementary multimodal sensor-fusion approach, utilizing camera, LiDAR, and inertial data for resilient robot pose estimation. Individual robot pose estimates are refined by a centralized multi-robot map-optimization approach to improve the reported location accuracy of detected objects of interest in the DARPA-defined coordinate frame. Furthermore, a unified exploration path-planning policy is presented to facilitate the autonomous operation of both legged and aerial robots in complex underground networks. Finally, to enable communication among team agents and the base station, CERBERUS utilizes a ground rover with a high-gain antenna and an optical fiber connection to the base station and wireless “breadcrumb” nodes deployed by the legged robots. We report results from the CERBERUS system-of-systems deployment at the DARPA Subterranean Challenge’s Tunnel and Urban Circuit events, along with the current limitations and the lessons learned for the benefit of the community.