Integrative research is increasingly a priority within the scientific community and is a central goal for the evolving field of sustainability science. While it is conceptually attractive, its successful implementation has been challenging and recent work suggests that the move towards interdisciplinarity and transdisciplinarity in sustainability science is being only partially realized. To address this from the perspective of social-ecological systems (SES) research, we examine the process of conducting a science of integration within the Southcentral Alaska Test Case (SCTC) of Alaska-EPSCoR as a test-bed for this approach. The SCTC is part of a large, 5 year, interdisciplinary study investigating changing environments and adaptations to those changes in Alaska. In this paper, we review progress toward a science of integration and present our efforts to confront the practical issues of applying proposed integration frameworks. We: (1) define our integration framework; (2) describe the collaborative processes, including the co-development of science through stakeholder engagement and partnerships; and (3) illustrate potential products of integrative, social-ecological systems research. The approaches we use can also be applied outside of this particular framework. We highlight challenges and propose improvements for integration in sustainability science by addressing the need for common frameworks and improved contextual understanding. These insights may be useful for capacity-building for interdisciplinary projects that address complex real-world social and environmental problems.