This game had a very Event Horizon feel to it. My belief is that you are the alien and the real captain is in the storage room. The alien was knocked out by the captain during a fight in which the alien was taking the captain's image. The alien must have been concussed and believed that it was the captain. The captain must have ran to the storage room and locked himself in there by accident and was trying to get help but when he heard his voice coming from the other side, he knew it was the alien which is why he didn't respond when the alien was asking who was in there. That's just my ending though I would have liked to see the author's ending.