I finally got to Atlantis and I'm stuck in the dark room (came through Teams path)

I cannot use the stones because "it's too dark" so I got the metal rod, but I'm now stuck. Every guide I saw they use "orichalcum beads" on the rod, but I don't seem to have any beads with me. I don't recall picking any up either. Is there something missing? some random event that seldom occurs? I recall this game having some randomizations

Is it possible you still have the golden box closed from when you were navigating through the labyrinth? You should have at least one orichalcum bead wtih you and I'm wondering if they're still in that box (the beads will only show up in your inventory when the box is open)

I saw no golden box in the labyrinth ¯\_(ツ)_/¯

And how where you able to use the amber fish to find the hidden door that leads to the model city where you use the three stones for the first time? If you don't have the box to put Sophia's necklace in it, the fish only points to Sophia.

I entered into the room with the hidden door, and used the fish. As Sophie was in the previous chamber and following me, I guess that the game didn't detect the necklace on her, thus pointing me directly to the door.

So, I discovered a bug? :O

I doubt the game actually checks if the Sophia sprite is on screen to allow or not the door to be detected by the fish. Since you have to go through the whole process of convincing Sophia to put the necklace in the box, and the box is taken out of the inventory completely (story wise, she has the box), there are much easier ways for it to check without possibility for error.

Upload your savegame here if you want.

Are you playing with the GOG release? A standalone ScummVM install? Original disks in real hardware?

Yeah I was using the GOG version with the bundled ScummVM, I 'fixed' it already by loading a previous save game, so I no longer have the original one with the stuck :(

If you want to try to replicate the incident, make sure to update ScummVM to the latest version before doing it (downloads here). Download one of the zip file versions and uncompress the files inside the ScummVM directory where the GOG version is installed.