This is for the intermission between A1 and A2.
I passed the persuasion check with his guard to let me into the cage, and all the "search his body" dialogue options with Alexander when he's sleeping do nothing. Pickpocketing him only show he's carrying a health potion. Killing and looting him also does nothing, nor does bumping up my wits to 21 and going through the dialogue tree again. I have reloaded from before the persuasion check and failed it purposely, killing the Magister guard to see if that changed anything.
Also, the living door on the left only tells me I have to enter from the other side, while the door on the right requires the gem (I already know the password). In addition, the other options to interact with the right-side door do nothing, so these are both dead ends without the gem.
I don't know what happened here, as this is my third full playthrough and I don't remember being stuck here like this, but for some reason I just never came across the strange gem this time.
I also had a save on Fort Joy that I reloaded to, and still had the same issue once I got back on the ship.
I believe I am soft-locked here, because I cannot loot the strange gem from Alexander, and that means I cannot enter the living doors (they cannot be lockpicked). Any help would be greatly appreciated. Thanks!