Final Cutscene?

I think he saw a alien.

A cheap scare.

Well basically she did not seems to be a transformed Necromorph, but mostly a decaying dead body. I must agree with Yellofellojp it was just a cheap scare and of course an hallucination.

-Nicole waited that long to attack Isaac in the cockpit, that don't make sense.
*But perhaps it was some super Necromorph since it was Nicole and blebleble....----->S*TF*U (Gamefaqs does not allow jokes about Senseless Troubled Freak Unitologists)

-Shuttle cockpit door was locked when Isaac got out and was still locked when he got in.
*But perhaps Nicole opened the door and accidentally locked it---->Who cares? They just never use the doors.

-Hive mind appears to be dead, so technically Necromorphs are all "dead reta*rded". (sry for the * but gamefaqs does not allow to insults directed towards Necromorphs--------->UNITOLOGISTS!!!!!!!!!!!!!!!!!
*But perhaps he is not dead----->He got killed by every gamers out there and he received a 100000000000 kg/tons pound rock on the face + EA did not show to me that he was still alive.

Some people surmise that it's because Issac still has the marker on board with him. What that actually means is left to be seen, but it could either be causing hallucinations for Issac, or controlling Nicole. Nicole may not necessarily be dead, because she could've injected a drug that makes her appear dead, considering her science background

The marker wasn't onboard the shuttle when you board it, its still outside on the pad waiting to be loaded. You never see Isaac load it onto the shuttle. As far as the end scene goes without regards to that, a necromorph in general would not wait that long to attack Isaac but would attack almost immediately. If it was Nicole would she have attacked him since she didn't appear to be anything more than a hallucination the last time you saw her, disappearing as she rounds the side of the marker. I think it was just EA ending the movie with a scare, there wasn't anything actually there at all. But like everyone's post before this one, what truly happened is not concrete and open for discussion and interpretation.

It was most likely a necromorph that was aboard his ship that attacked him.

I tawt I taw a putty cat!

Well i have seen the end cut scene on both pc and xbox 360. I have to say the pc version is better because. You can clearly see that it is Nicole in the xbox version but on the PC version i wasn't quite sure its looked see through so that leads me to the conclusion that it is all in his head. Although if you have read the posts on how the first letter of each chapter spell NICOLE IS DEAD. It might be a necromorph Nicole.... I like to think that the marker screwed with Isac's head big time and because its not back exactly where it waned to be or because Isac has killed the hive mind the marker is reaching out to make his brain go BOOM!! I think wait a little and all will be explained in the sequel. Lets hope EA keeps the same guys because this game was sex on a stick one of the most enjoyable games I've played in ages. Addictive too i couldn't stop playing but back to the question it is a hallucination of Nicole that's my guess.
Oh and for those of you who are trying to figure out what the message at the end says in Unitext it says Completed... I know, LAAME