Phased deactivation of functionality in implantable medical device systems

Embodiments of the invention are related to systems for interfacing with implantable medical devices, amongst other things. In an embodiment, the invention includes an external medical system including a processor and a telemetry circuit in communication with the processor, the processor configured to communicate with an implanted medical device. The system can be configured to query a system user after a first period of time in which indicators of system use are not detected. The system can be further configured to deactivate one or more data transmission features of the implanted medical device after a second period of time in which one or more indicators of system use are not detected. Other embodiments are also included herein.