It seems like the non activated portal next to Atheons door becomes much clearer once you start the gatekeeper fight and then come back through the door. The fogs have moved and it is very clear.
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Nothing is up with that gate. Its a broken theory.
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I think it more likely that we see more of it during a further DLC. But the second jumping puzzle doesn't make sense unless the portal is used for something
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The second jump puzzle is used to get up to atheons room without dying, after you reached the secret cave on the left side of the jumping maze. That's the biggest indicator for a triggert chest. The second jumping puzzle lets get you up to atheon after you took the chest
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It is being used for something. Bungie is using it so you sit here on reddit discussing what's its being used for. You see bungie is smart and they're keeping their game on your mind.
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Well lets hope that a higher difficulty helps on this matter.