Jeez, are we talking about the same black site? With the vial? I considered that part of the *tutorial*, I took it on basically right after I researched resistance comms. 4 rookies with ballistics and kevlar. It actually went really well though.
The facilities with the dots... I'm about 3-4 months in I think and just took out my first, using 5 magnetic kevlar troopers (mostly squaddies, because that's what I have). It was an absolute bloodbath, even with some savescumming, but the doom clock was 2 tiles away. Got two soldiers out, would have been three but ADVENT got lucky with reaction fire as she fled the building.
Hooray for Asia's $10 rookies... But I think this is turning around, finally, now that I have the training school and magnetic weapons. Basic armor, soon.
Lost 3 other soldiers on a retaliation mission, which I lost largely because the civvies were mostly spawned in a cluster across the map. I tried to hurry, but berserkers and necromancers take a little time to take out!! I did clear the map instead of withdrawing, though. I wonder if that mitigates the penalty a little (losing a retaliation doesn't seem to unliberate the zone, just permanently reduces their contribution)