Well, that doesn't really help much since the mission I'm trying to open can only open if the Midway is extremely damaged. My problem is I either kill the aliens too soon (not enough damage) or not soon enough and I fail entirely.
For your problem, I had the same one a few days ago. There's some beacon or something that's out there with you (it's a light blue on your radar). You have to fly real close to it and put out a bunch of mines. The ship you're flying should have a bunch of them (change to them by changing your missiles). Get in real close to it or it won't work. And if you get TOO close then you start taking damage. It's not bad though, so if you're ship is fine then you should be fine taking a little a damage also.