The syntax for the commands may be automatically generated through the GUI interface, entered directly into the command line interface (or shell) or provided in a command file. A natural language parser is used to make the best sense of your instructions but some units (especially military ones) will only respond to orders provided in a strict syntax and structure.

As the shell interface is based on Unix you may enter multiple commands on a line, separating them with a semi-colon e.g. reg1 move to Earth; reg1 muster 2000 troops; reg1 train as infantry would send each command in sequence to reg1, who would then respond in the best way possible.

The general syntax is as for addressing a third person in english or addressing a second person and asking them to communicate with a third person.
For example: Mombat order MombDiv1 to Mars would be parsed as noun phrase:Mombat (the name of the person), verb phrase: order MombDiv1 (the name of one of Mombat's units), with the remaining text passed as parameters for the verb phrase. As long as Mombat has authority over MombDiv1 this action be processed (if possible) once it has been transmitted over Galnet (which may take sometime).