Great concepts but many loose ends.

[i3670]

What bothers me more is that the mixture could dissolve the tissue leading to the refinery but not tissue on the giant gate to the outside so I could leave.

But then the shadow would've caught and killed you.

Nope it was after Alexander it wouldn't care.(I don't see why it would atleast)
But you were there for a reason you chose to forget so that you could stop Alexander without going crazy about torturing everything on your path making you emotionally weak.

But if you stay in the prison cell it will catch and kill you.