As far as the Transcendent's unfolding goes... that may have actually resulted in the Great Darkness! If you think about the necrosis of the manifold and the capacity for critters to emerge and devour dead bodies, the death of the Transcendent may have created the "Worm" we refer to as the "Great Darkness"
I wonder though what The Manifold is...and why would they use the word Necrosis?
Somewhere in Tenebra it was said that the Brahmans of old created a mistake, which now "stalks the cold corridors of the cosmos." Assuming that to be the G.D., then the Transcendant can't be the GD. He's not an ancient being, he was a modern human - he came from the GTVA, from the Sync Device (wait...was Sync made with Shivan tech?
). ... On the other hand, time has no meaning for him or the Vishnans, does it?
I think it's more likely that the Transcendant is a sort of rogue being, an independent, a relative or analogue to the GD, or a human-created facsimile of the GD. The GD may very well be the collective insanity of an entire transcended race (the Brahmans?). Is the Transcendant what would happen if the GD somehow 'escaped' Nagari? Or maybe he's a product of the GD? Perhaps the GD came first, the Sync Drive passed through it...and the Transcendant was thus "infected" by its insanity?
I theorized that, indirectly, the technicians may have observed the Great Darkness or it's effects on wherever it was. The transcendent may for all intents and purposes now serve as a "vessel" or "scout" for the GD. Or something else entirely.
Maybe the Transcendant is what happens if you look behind you.
EDIT: No wait. The Sync Device is an interdimensional transporter, whereas Nagari is a quantum pulse transmitter. Does the GD occupy a physical space? Does Nagari exist in a dimension unto itself? I suppose if your brain physically passes through dimensions, it's not all that different than having it receive data through dimensions? Maybe? Hmm. Now I'm stuck.
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Done.