Okay, I'm playing the main plot, mission 4, and just came upon something painfully stupid.
[mild spoilers]
I and an NPC are trying to escape the starting system and suddenly everyone and their cousin becomes hostile to us. Said NPC goes on about how we have to run and reach the jump gate. I charge my cruise engines and... Mission Failure: You have run from battle.
[/mild spoilers]
So despite the fact that in the story, the objective is to escape and avoid fighting, if you do so you'll lose the mission and you have to replay it until you destroy everything in your path.