As humans venture back to the Moon, or onward to near-Earth objects and Mars, it is expected that the rigors of this exploration will far exceed those of Apollo. Terrestrial analogs can play a key role in our preparations for these complex voyages, since in addition to their scientific value, analogs afford the exploration community a means to safely prepare and test exploration strategies for future robotic and human planetary missions. Many relevant analog studies exist, and each is focused on a particular aspect of strategic development. Some analog programs such as the Pavilion Lake Research Project (PLRP) present the opportunity to investigate both real scientific and real exploration scenarios in tandem. The activities of this research program demand the use of techniques, tools, and strategies for underwater scientific exploration, and the challenges associated with the scientific exploration of Pavilion Lake are analogous to those human explorers will encounter on other planetary and small solar system bodies. The goal of this paper is to provide a historical synopsis of the PLRP's objectives, milestones, and contributions to both the scientific and exploration community. Here, we focus on detailing the development and deployment of an integrated science and exploration program with analog application to our understanding of early Earth systems and the preparation for future human space exploration. Over a decade of exploration and discovery is chronicled herein.