Purpose: Canada's Chemical, Biological, Radiological, and Nuclear Research and Technology Initiative (CRTI) uses an operating model that is unusual in government. It is created to enable cross-boundary capability and capacity building and learning. Some consider it a model for other federal science initiatives. The purpose of this paper is to explore the nature of leadership--and its relationship to perceived effectiveness--in this complex network of counter-terrorism communities, where parts of the network are functioning better than others. At a more academic level, it explores whether complexity theory can inform leadership theory. Design/methodology/approach: This qualitative, empirical study uses phenomenography and elements of ethnography as methodologies. Data are gathered through interviews and observation. Findings: CRTI personnel refer to their initiative as a counter-terrorism network of communities. The leader of each community works--without positional authority--with participants from many organizations and locations. The paper reveals qualitatively different ways of understanding leadership. Even though CRTI groups have much in common, participants' ways of understanding that work vary greatly. Some understand their work environments as complex systems rather than as traditional government structures; this way of understanding is associated with perceptions of effectiveness. This finding can change the ways in which science and technology professionals make sense of their work in complex, trans-disciplinary fields such as counter-terrorism and global warming. Originality/value: This qualitative, empirical research complements and supports some of the conceptual work about leadership and learning in complex environments. (Contains 2 tables and 2 figures.)