Science diplomacy supposedly builds international cooperation through scientific and technical exchange. In practice, however, there are important but often overlooked instances where it might create conflict instead – as with accusations of espionage surrounding the US Naval Medical Research Unit 2 (NAMRU-2) in Indonesia. Did American science diplomacy backfire in Indonesia and, if so, why? Most literature fails to anticipate this possibility, let alone explain it, since science diplomacy is rarely subject to critical analysis. Rather than shun politics or, similarly, simply blame the demise of NAMRU-2 on the military or avian influenza, I consider both the successes and failures of this research unit in the context of Indonesia’s transition to democracy and America’s legacy from the Cold War. Based on this history, I propose that the effects of science diplomacy depend on strategic communication and exchange, as well as elite influence and material incentives. Therefore, by challenging the conventional wisdom about science diplomacy, NAMRU-2 can help advance the theory and practice of this potentially useful tool of statecraft.