I'm guessing most of what we saw was done for awhile and then cut and chopped up into dlc by activison. To accommodate these changes the story was probably removed along with several other things...I mean it was confirmed that Peter Dinklage recorded way more Ghost dialogue than what we saw. That's the reason so many people have left. They saw their work bastardized and Bungie shouldn't have made the deal they made, but those guys left in charge are bastards for sure. They let this happen and they are ok with it.
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I can agree with you there, many aspects of this game are clear, it shows that there were two heads thinking of one thing and you can see where it made a mess of it all. There is a saying that goes "Good employees don't quit their jobs, they quit their bosses." The new bosses are Activision, many of the founders of Bungie are gone, many of the Halo directors, Storyline creators are gone, and I honestly believe Activision is the cause.