Sorry for going off-topic, but need some clarification here. Are we talking about the events in Hephaestus? Because I've *always* ran instead of luring the patrol. The only pirates I encountered (not the scavengers whom you have to kill on the way) are the ones harassing that guy at the exit.

Edit: Oh, I see, he was trying to go *elsewhere* while that mission was still in progress? Yeah, I think the script auto-kills your mothership when you attempt to bail out during certain mission arcs. Sort of annoying.