Definetly not alone on that wondering. I think it was just a ceremony before they let someone else stab them to death. I kinda felt bad that Jacob Temple and Elizabeth ended up dying after you heard so much from them.

That just reminded me of something, maybe the ending of that story is supposed to be parallel to the Isaac/Nicole ending. As in one is already dead (when you reach that point) and the other dies soon after.

But if Nicole was an illusion the entire time, how would it be possible for her to open doors and push buttons for Isaac? After the beginning of chapter 12, she just disappears and probably just went back into the shuttle/ship. The player and Isaac kinda forgets about that because Kendra showed the full clip of Nicole injecting herself with something (which could be a lethal injection... OR possibly something else), thus making him think that she has died and he was just imagining things.

Other than that, we also can clearly see that Nicole did not look like any other Necromorph, which could also mean that she might not react or act like other Necromorphs.

Nicole was exactly where Isaac left her, and when he returned to the shuttle, it makes sense that she would still be there... and she was.

That actually seems reasonable because there is never a situation were Kendra would have seen her.

as far as what is animating her, it may have been the marker, but once the hive mind died it no longer controlled her, she became a zombie and started decaying

Did you watch the video when she kills herself? I think it is pretty clear that she is dead. How did "she" unlock doors? I do not have a satisfactory answer.

The only thing I can think you is the marker animating her, like a zombie,

Yeah, but there is no mention of zombies in the game...at least, zombies who look entirely alive and whole. Maybe Kendra was unlocking the door but Issac imagined it to be Nicole? 

That is exactly what I am thinking too. Kendra working on that door while you were shooting at imaginary things, cept the ones that dropped ammo and hit you, of course.

I'm still on the first level. lol. Too many games too little time.

 Well, there's 2 things to say about this.

1. No one knows what she injected herself with. It's a possibility that she did not have suicide in mind.

2. If she commited suicide, it's possible that something (we'll probably find out in DS2) reanimited or controled her body.

Other than that, how did Isaac bring the shuttle back to the hanger on chapter 11 without Nicole?

Also, another posibility could be that there were TWO nicoles running around.

1. The illusion Nicole that was caused by the marker. This one dissapeared when the marker was set.

2. A reanimated Nicole that was bing controled by the Hivemind. This one was on the shuttle and attacked Isaac when the Hivemind died.

It couldn't have been Kendra that opened the door, she was stilled isolated in the computer core at the time and specifically said she lost communication with Isaac for a few minutes once Nicole leaves,

Man I think this game's story was so well crafted, so many question that aren't derived from convultion but from tantilizing dangling plot lines, It stands so well on it's own yet was designed to beg for a sequel