The darkness is actually Cthulhu. [spoiler]Cthulhu confirmed[/spoiler]
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Half Life 3 confirmed
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It would actually be either The Nameless Mist, Ialdagorth, Haiogh-Yai, Ammutseba, The Blackness From The Stars, Aiueb Gnshal, or Azathoth. Just to name a few. All of those are outer gods (space gods basically) that have the description of a giant amorphous mass of either black mist, darkness, or void in the Cthulhu mythos. Cthulhu himself could be a giant enemy, I guess, but he doesn't live in space, he has lived on earth(in another dimension) for aeons... And he isn't made of darkness, his form, though gigantic and maddening, is still pretty linear.