I finally was able to capture a clipper, but I can't get it to do anything... How do I get it to attack my target? and after that, how do I make sure it doesn't blow it away before I can board it? The controls it gives in the game preferences don't seem to do much... forgive my ignorance...

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You pointin' that thing at me?

just to let you know clippers don't fight they just help carry your cargo. if you want a ship that fights get a lighting. also do you want a alien cruser?

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To order something to fight you have to have fighter bays, where you buy fighters.
crappy escorts like clippers will only attack things that attack them,
corvettes lightining and the such will attack things attacking you.
With fighters (use w and shift to select and use) target something and hit f...

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"Your attack has been rendered harmless.
It is, however, quite pretty"