Future military forces and platforms will be expected to operate within increasingly complex operational environments where the threats are diverse and increasingly challenging. This will increase the volumes and speed of data and information that commanders and platforms will need to capture, process and respond to. This will inevitably lead to the need for greater levels of automation and wider use of machine intelligence techniques across the Command and Control (C2) space. Over 3 phases the Intelligent Ship project has explored how Naval C2 can be designed to provide operational benefit from the introduction of collaborative teams of AI based agents delivering a range of function and roles, and how these teams can be effectively integrated with Human operators to form Human Autonomy Teams (HAT). This paper will provide an update of the project and summarize and discuss the additional lessons learnt and challenges identified during Phase 3 due to complete in January 2025. This phase has placed a greater focus on the Human aspects of HAT, in particular that the needs of capabilities of the ‘responsible and accountable’ humans are designed into the collaborative-system from the start. This is being achieved through the investigation of various design and optimization approaches, including cross-AI/human team arbitration techniques. The project is again using simulation capabilities (cloud and Dstl lab based) to test approaches and designs against aspects of Naval C2 for Anti-Air Warfare (AAW). The paper will discuss the design approaches, the evaluation aims and preliminary results and conclusions, aiming to provide an insight into some of the key factors implicit in effective HAT design.