I'm having the same problem. Was in the middle of things, when NPC's started randomly going invis and warping through floors and walls. I managed to kill them anyway, turned off the alarms, got to the room with the round hole in the ceiling directly below the Command Center, and for some reason, there's no way up. Everything's dead, no fighting, no alarms, nothing to do but run around. Saved the game, rebooted, and still stuck. Dang.
