The AEGIS (Autonomous Exploration for Gathering Increased Science) intelligent targeting software system has been in use on the Mars Science Laboratory (MSL) mission since 2016. The system allows on-board autonomous selection of targets for the ChemCam remote geochemistry instrument based on analysis of images taken by the rover. This paper describes the deployment of AEGIS to MSL and the operational use of the system since rollout to science operations in May of 2016. We describe how MSL Science Operations have adapted to include autonomous target selection, both in procedures and in exploration strategies, and how mission planners and scientists have used AEGIS autonomy to enhance their work on the MSL mission.