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                               - Choices -
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- Bud -
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In Part D of the Prologue, you will be given the choice of whether to stop Bud 
(the marine) by stunning him or by killing him.  If you decide to kill him 
then the Marines throughout Chapter 1 will lend little support during the 
Seeker battle, however if you stun him they will help you blast the Seekers.

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- Ethan or Olivia -
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In the final part of Chapter 1 Part E, you're given the choice of who to take 
with you to the escape pod.  This choice will affect quite a few cutscenes 
throughout the rest of the game and will affect the appearance of the final 
boss in the Epilogue.