Well it looked like some of the the people were being crushed and made into egg shapes. But i guess with that many eggs it could have been a queen deeper in the core than we went. The eggs did look just like the movie though which was awesome..
Also i was afraid to use anything against the alien for fear of it learning. It did stop responding to the flares as well as it used to, In the beginning it would entrance it for 5+seconds, and by the end it would walk over to it, stare at it for a second and walk away, chase and kill me.. I tried to limit the amount of times i used the flame thrower on it, never used a noise maker on it, or pipe bomb or Molotov.
But there were a ton of people missing and a dozens of aliens so it could have been egg morphing. IF we could pick levels to play that would be easier, but unfortunatly having to play through the entire game to see certain parts sorta sucks.
Spoiler