OK, I'm gonna jump in uninvited with an F of a lot of points here, some of them may be misguided or uninformed (this coming from the background of Downfall as well, so I'm not sure how canon):
- Kendra is a government agent, but what exactly is her mission? How much was Kendra manipulating Isaac Couldn't a message have been sent to the Valor without being aboard the Ishimura? Did the gov. want to destroy the marker or retrieve it?
- What was the purpose of the second marker? What did the government hope to gain from it? Were the Necros there before it? Was it designed to keep them there?
- What happened to the original marker? What did it do? Where is it now? Who built it?
- Did the hallucinations come from Hive Mind or Marker? Do Hive Mind and Marker have the same agenda?
- Were the Unitoligists (loved the parallels with Scientology) really just a misguided group, who'd somehow got wind of the original marker and formed a religion around it, or is there something more sinister at work in its upper echelons?
- Was Hammond really innocent? Did he have his own agenda, other than repairing the Ishimura and getting the Hell out?
- Does Necrole kill Isaac at the end or could he have fought her/it off?
I realise that many of these questions are unaswerable as none of the elements of the Dead Space franchise provide the information, but it was all on my mind and I was wondering what people thought
My views are that the government found Aegis 7 and the Necromorphs and built the marker to leave them dormant on the planet protecting the rest of the galaxy; if this is the case then it is possible that the original marker, which was found on Earth was designed by an ancient alien race who had found Earth and observed humanity's violent and cruel tendencies and left the marker there to stop humanity spreading throughout the galaxy, but it only succeeded in slowing the human race not stopping it entirely, meaning that eventually the Necros could break free of the marker's power (of course this all just conjecture).
Nicole was dead before Isaac arrived at the Ishimura. The Nicole seen throughout the game is a hallucination; the locked door which she opens is also a hallucination, as is the attack by Necros. The game over is triggered because Isaac believes entirely in the hallucination and believes there is no way forward, coupled with the apparent death of his girlfriend he would be distraught and despondent and easily ready to admit defeat (i.e. give up).
The marker was designed to keep the Necros on Aegis 7 therefore manipulates Isaac into returning it to the planet's surface to fulfil its purpose. The Hive Mind tries to prevent this to protect her newfound freedom.
I really hope Isaac is alive so he can come back for Aliens style sequel where no one believes him and he has to assist the military, mainly because I think it would be cool to see some squad based survival/horror and maybe some co-op, but that might take the fright out of it.