The authors draw on their experience with the autonomy technology demonstration on NASA's Deep Space One mission to describe the wide-ranging effect autonomy will have on the development of spacecraft software. Autonomy technology for high-level, closed-loop control of spacecraft offers considerable benefits to space-flight projects. Those benefits can enable whole new classes of missions; however, they are not without cost. In this article, they describe both the impact that autonomy technology has on spacecraft software and the implications for the software architecture that arise from those impacts. Some of the impacts are inherent in the challenging problems generally confronted in the spacecraft domain yet are exacerbated by autonomy technology.