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None of the other Halo games had a pattern, so it seemed odd that there would be one for Halo 2.
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It might seem odd because Bungie wanted to put in Arbiter's story while having a balance with Chief's. Pairs of missions were an effective way of doing this.
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Also, I think that for the last four missions, they weren't originally supposed to be split up like that. Chronologically it doesn't make sense, as at the end of Uprising, we see Tartarus's Phantom landing, but at the beginning of the next mission (High Charity), we see it [i]leaving[/i], which means that Uprising and High Charity take place simultaneously, which doesn't actually make any sense, given that the Arbiter and the Master Chief should have been teleported at the same time, which means that Gravemind and Uprising should be happening at the same time.
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I can't believe I've never noticed that before... Damn it, I've been playing Halo 2 since 2004 and I never noticed that.
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Here's a better question: The entirety of Quarantine Zone is based of the arbitrary (see what I did there) rule that the Phantom that drops off reinforcements at the beginning can't just pick you up and fly you to the library, even though it is capable of flying with the Gondala the entire time.
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I just assumed that was Tartarus subtly trying to get Thel killed and Thel proving he was a BAMF.
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That's what I was thinking. That's kind of the point of becoming an Arbiter.