Wowww....that was it haha. Numerous thanks, I never realized that the "don't move directive" wasn't directed to the pirates. I thought it was to the pirates, and that they didnt listen at which point someone says "now they're onto us!" so i always just went out all 7k and destroyed em haha. And i don't know, for what ever reason whenever I was detected and the hubble was still around, after two waves of 4 pirates, nothing would happen for the rest of the mission and I would just sit there. Thanks again.
Edit: I just played a little more, and I'm getting the same problem as bustrobot. Except, for me it seems to be semi problematic because i jump in with only 1% health so invariably i die at some point or the other. It happened on the other red alert mission too but i managed to make it through that mission without touching anything, but here (after trailblazers) it seems harder, so help would b appreciated. Thanks