About 4 or 5 times after his head was open I heard a different pain sound. I was aiming for a gap where his head was open, and moving the aim around a little bit continually to vary where my shots were landing. Then keep shooting the top of his head with the alt fire of the hive hand (which is explosive). Then shoot the top of his head with the Hive-hand until the top of his head opens up. Hide behind one of the pillars, take out the 3 orange crystals first with the cross-bow (alt fire zooms).
I just stayed hidden behind one of the pillars the whole time, although you have to occasionally kill an enemy because when the green orbs hit the pillar they convert to an Alien Slave or an Alien Controller. I just finished the Source version just now, and you don't have to get above him, or go to any of the teleport rooms either.
