What the story needed [SPOILER]

[Kein]

Unhandled

What is the Kaernk water beast?

ALEXANDER: "Not without a way to ward off the guard dogs. Oh my! How they make such a splash. But don't worry, you're with me, and not all alone, right?"

You are wrong. Alexander can't control them, it's a creature from the other world and only Weyer was skilled enough to bring it here, in our world, to Alexander.

Who is Agrippa? Who is Weyer?

Huh?
You didn't notice? The Alexander tried to hide as much as possiblr from Daniel. The latter was just a pawn with Orb in his hands. And the Orb is only thing Alexander was after.
Helping Daniel? Ha, he couldn't care less. Telling about Agrippa and Weyer and other world? Lol, no way.

I thought it might be this organic tissue just suddenly appearing all over the place.

Wow, I'm 999% sure this is a wild guess but you are right here. The organic things represents a Shadow's realm. Noted in PDF from super_secret.rar.

ChrisSmith

Explaining the enemies is completely unnecessary [...]

... if they do make sense by default. But Amnesia's ones do not. What is the use of scary Grunt/Brutes with undeveloped arms? To watch out for prisoners? Are u kidding me? The prisoner is near to death or, either, very weak to make any escape, also, there isn't so much left.
Serving Alexander his dinner, helping in experiments? Barely doubt, they are like stupid dolls that can be controlled and no more.
So I agree here with Unhandled, a bit more SENSE and explanation is welcome. Because a monster just for a monster is silly and we either must accept this as a stupid thing in the setting or exclude from it and count only as a gameplay (story/setting-unrelated) aspect.

Harry

In case you've never read a Lovecraft or Poe

As a first game from Frictional, the Penumbra was ok with this way, but Amnesia is boring already. I think Frics must do something original, not repeating himself.