Run around the Boss in a circle while shooting it with the machine gun. When it is low on health, use the flame thrower to finish it off. If done correctly, you can kill it without being hit. After you kill the Boss, the Thing in the glass in the room will break out, and the door will be opened with a few guards.

This Boss has a sweet spot. If you get directly under it, it will not attack. When you get under it, blast away until its health is in the red, then burn it.