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A sneaky opponent dastardly disabled my weapons - so I am in this fight where my only attack is that my weak clone can tickle his shield a bit - my men can only run about and put out fires.

Time to give up? Or should I try and hold on, hoping for some kind of miracle?
Don't give up the run unless there is no way to survive the battle. Either by fixing your weapons (if possible) or waiting long enough to be able to jump to the next beacon and hope it's peaceful. Good luck!
oh thank! I forgot about jump!

(and then I reached that mothership for the first time and got killed. Oh well...)