Includes supplemental material / Hostile acts of maritime piracy and terrorism have increased worldwide in recent years, and the global impacts of a successful attack on commercial shipping in the Straits of Malacca make it one of the most tempting target locations for maritime terrorism. In an attempt to develop a system of systems to defeat and prevent terrorism in the Straits of Malacca, this study developed three significant commercial shipping attack scenarios (Weapons of Mass Destruction (WMD) shipment, Ship As a Weapon (SAW), and Small Boat Attack (SBA)), and used a Systems Engineering Design Process (SEDP) to design alternative architectures that offered promising ways to defeat these attacks. Maritime Domain Protection (MDP) architecture alternatives combined five separate systems: a Land Inspection System, a Sensor System, a Command and Control, Communications, and Intelligence (C3I) System, a Response Force System, and a Sea Inspection System. Individual models for each system were developed and combined into overarching integrated architecture models to evaluate overall performance. The study results showed that solutions tended to be threat-specific, and current capabilities were mixed. While solutions were found to effectively reduce risk in all threat scenarios, these sometimes came at great expense. Alternatively, cost-effective solutions were also found for each scenario, but these sometimes gave limited performance.