Potential spoilers The idea behind this, was the research facility is conducting experiments (kinda resi mixed with half life vibes). So the buildings you could see are more for the low level staff of Nova Nexus, the higher level staff who do all the big research and experiments are in an underground base (this is why when the explosion happens you never see fire or smoke from the buildings as it was underground). The experiment goes totally wrong and that is when  the calls start happening. The thing that happens awakes a sort of ghostly demon monster from another plane and that is why the base is shut down and 'Kill everything' protocol is activated so nothing gets out. 


In regards to the endings. 

With Ending 1, The Car that lands on the broken down car was chucked by the demon monster thing from the car park. So basically - it got out!

Ending 2 is the phones calling the families of the dead. You're the phone near the screen. The big thing that comes out of the base is something that basically creates a massive creator in that part of the world.

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