It's one of those things with the antennae taking pot shots from a roof, dodging around the ducts and stuff. It was sniping and hitting my guys who were facing it but unable to see it.
Suppressing machine-gun laser fire didn't work, it was all blocked to 0% effect by the air conditioning ducting.
Eventually I tossed more or less every grenade I had onto the roof and the fire ceased. At the end of the mission I was told I'd killed all the aliens, so obviously the plastering with grenades worked, but at no stage did I see the actual alien, just bolts of fire during the aliens' turn. Very annoying.
I have a tank now, so maybe that will help another time. Failing that, I'd just have to capture the ship, and wait out till I win that way. The trouble was, this alien shot my guys in the back as they ran from cover to the ship. And if Rooftop Sniper Guy didn't kill them, someone else did as soon as the doors opened.