SPOILERS LIKE WHOA BELOW.
Well I figured she'd killed herself already. The video that Isaac watches in the beginning cuts off way too early to be the end of the actual film she recorded. I didn't know how she died, but I knew she was dead. I pieced the bit about the marker being able to control things through the first few chapters, especially when Kendra talks about her brother. The main thing about the story I didn't like was "how the heck can the entire ship but 4 people be dead, and how can those 4 people safely travel from place to place on a giant ship infested with aliens?" It was right at the part when Nichole was opening the door for me that I knew a) she wasn't alive/she was a hallucination and b) the Hive Mind was partially controlling Isaac already.
Wikipedia says, at the end of the story section, "As he sets course away from Aegis VII, Clarke thinks about Nicole and is attacked by her as a Necromorph; however, the event is revealed to be another hallucination as Issac takes off his helmet." The way I remember the ending was Isaac takes his helmet off, shakes his head a bit, deletes the Nichole video, notices something out of the corner of his eye, looks, is then attacked, and the screen goes black.
I really enjoyed this game. The story is the best story for a 1ps I've played in quite some time. I want to go back and piece together all the audio, video and text logs, so that I can get a fuller picture of the game.
Extremely fun. I'm playing it again on New Game+ and flew through the first two chapters. Going to try to get as many achievements as possible this go 'round.