This paper describes new autonomy technology that enabled a team of unmanned surface vehicles (USVs) to execute cooperative behaviors in the USV Swarm II harbor patrol demonstration and provides a description of autonomy performance in the event. The new developments extend the NASA Jet Propulsion Laboratory’s CARACaS (Control Architecture for Robotic Agent Command and Sensing) autonomy architecture, which provides foundational software infrastructure, core executive functions, and several default robotic technology modules. In Swarm II, CARACaS demonstrated higher levels of autonomy and more complex cooperation than previous on-water exercises, using full-sized vehicles and real-world sensing and communication. The core autonomous behaviors to support the harbor patrol scenario included Patrol, Track, Inspect, and Trail, providing the capability of finding all vessels entering the patrol area, keeping track of them, inspecting them to infer intent, and trailing suspect vessels. Significantly, CARACaS assumed responsibility for not only executing tasks safely and efficiently but also recognizing what tasks needed to be accomplished, given the current state of the world. Since the heterogeneous USV teams shared world model that evolved, such as due to (dis)appearance of vessels in the area or a change in health or availability of a USV, CARACaS replanned to generate and reallocate the new task list. Thus, human intervention was never required in the loop to task USVs during mission execution, though a supervisory role was supported in the autonomy system for mission monitoring and exception handling. Finally, CARACaS also ensured the USVs avoided hazards and obeyed the applicable rules of the road, using its local motion planning modules.