1) To retrieve the marker. When she was sent, the government had probably hoped the team would arrive at Ishimura before all hell broke lose. If they known an outbreak had already occurred, i speculate they would have sent Valor in for an immediate attack and not even go through the facade of sending a repair team with an embedded agent on-board.
2) I think the second marker was manufactured to trap the necromorphs on the planet. I am confused though on how a man-made replica of the marker can still have the same psychic effect on humans as the original marker. The government must have backward engineered how the original marker worked completely to build a marker copy that worked as well. Plus the marker appears sentient which makes it even more weird that its a man-made copy.
3) I think the original marker is still in the hands of the goverment being studied.
4) The Marker was behind Isaac's hallucinations.
5) A group that believes the necromorphs are the next stage of human evolution are extrememly dangerous despite their pure intentions. I didn't see any records or audio tapes that mentioned if the church leadership are true-believers or cynically pulling strings for a different purpose.
6) Dude was just doing his job. Although if I were him, I wouldn't have left Isaac's side. Engage necromorphs Army of Two style.
7) Like everyone else, I heard that Isaac isn't dead. I agree with the_A_drain on why the ending is in there. It was probably just an hallucination brought on by stress and guilt since I thought the necromorphs were all inactive now that the marker had been returned to the planet - and the hive mind getting slammed by the planet core.
I'm not sure how you implement a co-op or squad mode and keep the same atmosphere to the game. I think the dead space universe is rich enough to allow for an awesome franchise though. Since the Ishimura was as much a character as Isaac and Kendra, the sequel would need a compelling environment as well. I like super_machine's idea of a mausoleum ship.
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