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Hmm, I didn't notice it before, but just before you teleport to Nilihath ( The Final Boss ) via the Red Portal, stand for a moment and listen inside the incense (?) burners area.
You'll hear things from the beginning of the game :
" We tried to warn them " - Scientist
" Gordon, you're alright, thank god ..... etc"
I wonder if this somehow ties in with HL2 .........