The Caragot

 was a mysterious being which the Valeyard knew. They had bonded cybernetic armour. They could integrate other beings and tried this with Bernice Summerfield and Liyi to gain their intelligence. They wanted to integrate the Valeyard. They were incapable of forming a proper plan and that's why they wanted the Valeyard, thinking he was the Doctor. They absorbed Liyi and used her knowledge to manipulate the tunnels. (AUDIO: Every Dark Thought)