I love the fact that people are exploring for hidden secrets in the vault. It is one of the few things that is actually interesting about the game mostly because there is so much we dont know about the lore of the game.
So in order to share my own to cents i will contribute to some theories and then present my own theory. Now before i do i feel the need to say that i dont think there is anything to find mostly because people have tried so many crazy ideas but it is still worth looking into.
1st... Kabr's ghost. Now it is not entirely impossible that Kabr's ghost is out there, his ghost has not been destroyed at least not that we know of. All we know is that the grimoire says his ghost was taken most likely from the vex so it may be worth looking for.
2nd...The infamous 3rd jumping puzzle and portal outside the gatekeeper. A personal favorite many people believe including myself that if there is anything out there is has to be there. Sadly i dont think the third puzzle has been confirmed but many people state it exists so i believe it does as well. What the portal leads to or what it holds or if it can even be opened is unknown but there might be something there.
3rd... The oracles specifically before the templar part. Some believe destroying them in a specific order ( not in order they spawn, that has been disproven i think ) could activate something maybe in musical order, or any other ways i cant think of right now.
My own theory is that if there is anything at all left for us to find it has to do with the jumping puzzle, it is the only thing that does not give a reward after except for confluxes of course. Maybe its hidden, personally i believe that it needs to be triggered, but it may need two different triggers, people have claimed that the third puzzle exists but no one really knows how its activated, and then of course there is the chest trigger that perhaps cant even happen without the puzzle being triggered? Who knows there are many different possibilities, perhaps getting spotted by all gorgons at once? Maybe killing oracles in a specific manner, maybe actually letting the templar teleport?
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I found something cool you might wanna see this
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I'll be exploring the VOG on the 360 tomorrow if anyone wants in. Same GT as here. Just lemme know by sending me a message on XBL.