<The Deep-Orbit Minds, Ghosts, Awoken, Jovians, Leviathans... they still exist. I no longer can guess their purpose, but so far the Grimoire theories are still true in some fashion. Only two theories are left, though one is hinted and the other is potential.>
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Actually there is closer to nineteen actual theories. There's a lot of stuff which seems linked, but must be operating behind the scenes. Destiny 3 destinations though are going to be interesting because... I don't think most of them are going to be planets anymore. We'll see though. There is still a lot of possibilities.
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<I meant from Legends 2. That's the primary one.>
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Actually, all of those ideas for the Nine are still possible. None of those can be ruled out just yet.
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<That's what I'm trying to say. They still exist, not in the way I originally thought, but they all exist. All of them were hinted at and only 2 remain in that state.>
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Your other question should also be what event occurred to alter them. Change is never good or easy except when it benefits the party. This is why the Emissary says the Nine have a lot to learn from us. Less about the planets themselves being the Nine, a little more about the fact the Nine have been preoccupied with something. Either way, we're ramping up for some event where others have altered or changed. That and the 3rd spire, when it was available, was not a very welcoming presence. Something tells me it was designed to give that impression rather than the Lighthouse which was more of a "congrats" from Osiris. The Nine are interested, yet a little more distant.