Command and Data Handling (C&DH) is essentially the “brains” behind the spacecraft. C&DH controls all autonomous actions made by the satellite, all uplinked/downlinked communications, and tracks the spacecraft time. Selecting appropriate CPUs and microcontrollers is critical, as is programming the operating system and lower-level functions. It also controls the decision making capabilities of the spacecraft. All data that are needed for any function of the satellite passes through this subsystem. Command and Data Handling is critical for mission success; without it the satellite would not function.

For the M3 program the code for C&DH is programmed in such a way that it completes the concept of operations (CONOPS) for the mission. The flight computer issues all commands to each subsystem, including initiating subsystem resets and managing the transfer of data between the subsystems. The flight computer also is able to change between Chemical and Electrical thruster modes autonomously. Additionally, the flight computer compiles any data deemed necessary by CONOPS and transmits that data to the ground station.

In order to communicate with all of the various circuit boards and sensors on the MR & MRS SAT spacecraft the C&DH system makes use of multiple data buses. Also, because MR SAT will have limited ground station access during the mission, the spacecraft must be able to switch between mission modes and execute functions autonomously. To do this the flight code contains a class called the StateMachine that mangages transitions between mission modes and the functions of C&DH in the respective modes.