Out of the box, X: Rebirth does not give you many options for controlling ships that you own. Have no fear though, the intrepid modding community has already started work on a solution. Introducing the Manual Command Extension!
Included at the time of this writing: Hold your Position, Move to My Position and Follow Me. The ships have to be in your squad, but other than that you can give them rudimentary commands! It's a great start considering the game has only been out a few days.
You can find all the details here: http://forum.egosoft.com/viewtopic.php?t=350741&postdays=0&postorder=asc&start=0
New Arc Line - Early Access Release
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