With the ending of the Cold War, the US Department of Energy is responsible for the remediation of radioactive waste and disposal of land no longer needed for nuclear material production or related national security missions. The task of characterizing the hazards and risks from radionuclides is necessary for assuring the protection of health of humans and the environment. This is a particularly daunting task for those sites that had underground testing of nuclear weapons, where the radioactive contamination is currently inaccessible. Herein we report on the development of a Science Plan to characterize the physical and biological marine environment around Amchitka Island in the Aleutian chain of Alaska, where three underground nuclear tests were conducted (1965-1971). Information on the ecology, geology, and current radionuclide levels in biota, water, and sediment is necessary for evaluating possible current contamination and to serve as a baseline for developing a plan to ensure human and ecosystem health in perpetuity. Other information required includes identifying the location of the salt water/fresh water interface where migration to the ocean might occur in the future and determining groundwater recharge balances, as well as assessing other physical/geological features of Amchitka near the test sites. The Science Plan is needed to address the confusing and conflicting information available to the public about radionuclide risks from underground nuclear blasts in the late 1960s and early 1970s, as well as the potential for volcanic or seismic activity to disrupt shot cavities or accelerate migration of radionuclides into the sea. Developing a Science Plan involved agreement among regulators and other stakeholders, assignment of the task to the Consortium for Risk Evaluation with Stakeholder Participation, and development of a consensus Science Plan that dealt with contentious scientific issues. Involvement of the regulators (State of Alaska), resource trustees (U S Fish and Wildlife Service), representatives of the Aleut and Pribilof Island communities, and other stakeholders was essential for plan development and approval, although this created tensions because of the different objectives of each group. The complicated process of developing a Science Plan involved iterations and interactions with multiple agencies and organizations, scientists in several disciplines, regulators, and the participation of Aleut people in their home communities, as well as the general public. The importance of including all parties in all phases of the development of the Science Plan was critical to its acceptance by a broad range of regulators, agencies, resource trustees, Aleutian/Pribilof communities, and other stakeholders.