MotionBuilder can be run in batch mode, letting you execute commands without the interface. To do so, the -batch flag must be used when starting MotionBuilder. The batch flag is usually used for executing a Python script, which can be set with the -F flag.
The -batch flag starts MotionBuilder, executes any commands you specify, and then closes MotionBuilder. For example, you could create a script to open a file from a previous version of MotionBuilder in order to update it to the current version.