The defense of a naval ship berthed in a harbor is a complex task affected by many factors. These include the fishing vessel density close to the ship and the challenge of discriminating neutral vessels from threats. A naval vessel berthed at harbor is more susceptible to attack than a vessel in open seas. The chances of detecting and countering a terrorist boat vary widely depending on several factors, including early identification of the attack and weapons available. This research uses modeling in Map Aware Non-uniform Automata MANA to analyze the protection measures adopted by naval vessels against terrorist boats. Design of experiments is used to efficiently generate data, which is then replicated using high-performance computing, to address a wide range of possibilities and outcomes. The data generated is analyzed using a variety of techniques. The study concludes that lethality of Blue weapons is the most important factor in determining Blues ability to counter a Red suicide boat attack. Additionally, the tactic of firing a warning shot followed by disabling shots within the exclusion zone decreases Blues success probability. Finally, an exclusion zone of at least 60 meters that is enforced with a patrol boat is recommended.