In 1986, Hamerton-Kelly resigned from Memorial Church and became a Senior Research Scholar at the Center for International Security and Arms Control (now the Center for International Security and Cooperation). In this capacity, he focused on the ethical issues raised by nuclear weapons and other aspects of military intervention. Hamerton-Kelly was particularly interested in ethnic conflict in Central Europe, in particular the role of religion in these conflicts. He traveled extensively in Central Europe during the early 1990s, shortly after the Revolutions of 1989 had created unprecedented democratization of the region, but which also exposed ethnic friction.