To be more precise, in the comic the God Machine doesn't work at all - it NEVER DID. It wasn't a matter of putting in the right amount of Orichalcum beads - the God Machine was just a failed experiment created through the mad hubris of a decaying civilization attempting to ascend to the same level as their alien "gods". Unlike the game, where the Energy Being endings hints that the Atlanteans were on to something, in the comics, it was all utter nonsense!
There's an earlier moment in the comic where an Orichalcum-powered statue advances on the characters, only to trip over its own feet and shatter on the floor (which is noted by Sophia) that gives a kind of disturbing foreshadowing to the true nature of the God Machine - that all the wondrous technology of Atlantis is just barely comprehended imitations of real technology, because aside from the Orichalcum, which the aliens gave to the Atlanteans, none of it is really anything other than Bronze Age knockoffs of advanced tech. The glittering utopian legend of Atlantis is nothing but a pathetic Cargo Cult.
In the game, the inner circles of Atlantis start to become this as time goes by, especially if you haven't rescued Sophia yet. Up until now, the Lost City hasn't seemed too frightening; the hallways are immensely wide and brightly lit, the ruined architecture is a little too grand to be frightening, and the Nazis are always patrolling the area to provide a reassuring series of fist-fights. After the canals, however, the random encounters end, and you're allowed to wander freely through the dimly-lit claustrophobic hallways of the second circle, all alone except for the eerie carvings on the walls and the skeletons on the ground.
Another element that adds a layer to the creepiness factor: the skeletons themselves. Maybe it's just the graphics, but quite a few of them look as though they died screaming in agony. If you decide to examine the bones, you can hearthe uneasiness in Indy's voice as he describes them.
Maybe they're animal bones.
No animal I know about has bones like these...
These bones are weirdly twisted.
Any human being with bones like this had to have been diseased.
It becomes especially so when by the end of the game it becomes clear that what Kerner became is about the same as the skeletons on the ground. The skeletons are the failed experiments from the God machine.
The canals themselves are guarded by a giant octopus.
There's a Dummied Out death where Indy enters the canal and gets eaten by said octopus.
When Sophia first puts the bead in her pendant and Nur-Ab-Sal appears for a brief second. It's not exactly nightmare fuel, but genuinely creepy.
It's even worse when you put a bead in her pendant while she's possessed. Suddenly, the pendant's face changes to give you a creepy Slasher Smile.
Sophia'spossession by Nur-Ab-Sal. It's even hinted at through the game at certain points where she'll start speaking in a deep masculine voice briefly if you choose certain lines of dialogue.
The Greater Colony. A dark labyrinth filled with the remains of previous explorers, including Sternhart. Although you can't actually starve to death in the game, it feels imminent if you don't find a way out. You're also completely alone, except in the Fists path, where there are plenty of Nazis to keep you company.
