Jurgen Leitner! He has been living in the tunnels since his library burned down, and was in contact with Gertrude when she was still alive. He uses books ('The Seven Lamps of Achitecture' and 'A Disappearance') to change the tunnels and to hide himself from Jon's 'master'.
Jurgen mentions 'Powers' or 'Entities', beings of vast, dark power. The way he explains this is incredibly vague, so I'll do my best to explain this a little bit (though not more than what he talks about obviously).
There are multiple Powers or Entities, and each of them manifest in mulitple ways, for example as creatures, monsters, artifacts or books. Jurgen does not specify how many there are, but he does identify some of them:
'The Spiral', also called 'it is lies' or 'it is lying'. A part of this is the Distortion, which we know as Michael (the door). The Spiral is about fooling the senses, making you see and hear things that aren't there, mazes, making you doubt your own sanity, fractals.
'The Eye', also called 'Beholding'. Everyone in the institute belongs to the eye, and Elias is at the heart of this (the institute is 'his place of power' according to Jurgen). The Eye is also who Jurgen refers to when he talks about 'Jon's master'.
'The Stranger'. Gertrude was looking into this. They are planning something called 'the Unknowing'.