The Facility is a massive research centre which contains the sectors 2, 3, 4 and probably the City. It is ran by the scientists and the masked men. A research focused on mind control since the discovery (or synthesis) of the worms/parasites. The central core of the research is the Huddle, a powerful amalgamation of different human bodies and minds that might control the husks.
In the game, the Protagonist encounters several hazards suspiciously placed to obstruct the access to the Huddle. This can indicate that the whole round was designed as an experiment. It tests the intelligence of the Huddle by selecting the best husks to merge with it at the water chamber (sector 4).