Why do we only see the stranger in the main story? Seriously, did Bungie just put her in as a filler character?
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This game is slowly evolving over a long period. Lot of lose holes will be tied up as more expansions come out. Remover Halo did have a lot of plot holes also that some didn't make sense until the later games. This game has a good foundation for a great story. They just seemed to have rushed the first part of it or wanted to stretch it out really far.