On one hand, it is cool that you are putting the pieces together, on the other though you have to remember that the lead writer left half way through development so I dont think everything was going according to plan.
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Yeah, basically my theory is that after he left, they couldn't finish the story and make it coherent enough (it would kinda be like a book switching authors halfway through) and they didn't have enough time to write and produce a brand new one, so they left it for us to discover. Kinda like a lot of stuff in the game that you're left to figure out on your own (i.e. the VoG)