I just replayed the 1st mission again and noticing the dialogue. Considering we know now that Savathun had her memories erased, probably had her Hive followers remember some about they're relationship-- they were their version of "The Last City". On first meeting, we killed the Hive guardian (probably no worries) but then [b]we killed the Hive ghost[/b]. And Savathun was referring to us as "honored guests" and not as usual 'guardians' but at the same time I think [b]she had sensed some Darkness in us[/b] because of Stasis and so we were strangers to her that came and attacked her people and killed a ghost-- something that "mirrors us" she said. These [b]Lucent Hive were pure Light[/b] already and we were half Light half Dark.
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We have to keep in mind [u][b]Savathun was basically "reset" into a fresh new guardian[/b][/u] and she wasn't who she was before and during season of the lost (much like Crow). Despite how devious Savathun's personality seems, she's still like a good leader supposedly trying to protect her people and the Traveler. I think in their eyes (and even objectively) we were the 'bad guys' in this one.
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My favorite thing about her, one of her memories; she realized conquering everything, or to be the last living thing was overall pointless...what then really? I saved the clip, because it's how I explain an AI, and how we demonize them often times. Like the AI in wargames realized that nuclear war was pointless, no winner. And what the "Witness" has realized...existence with life and death is pointless.