Onboard autonomy technologies such as planning and scheduling, identification of scientific targets, and content-based data summarization, will lead to exciting new space science missions. However, the challenge of operating missions with such onboard autonomous capabilities has not been studied to a level of detail sufficient for consideration in mission concepts. These autonomy capabilities will require changes to current operations processes, practices, and tools. We have developed a case study to assess the changes needed to enable operators and scientists to operate an autonomous spacecraft by facilitating a common model between the ground personnel and the onboard algorithms. We assess the new operations tools and workflows necessary to enable operators and scientists to convey their desired intent to the spacecraft, and to be able to reconstruct and explain the decisions made onboard and the state of the spacecraft. Mock-ups of these tools were used in a user study to understand the effectiveness of the processes and tools in enabling a shared framework of understanding, and in the ability of the operators and scientists to effectively achieve mission science objectives.