Jonathan Sims is tired and not fully recovered from Jane Prentiss' attack on the Archives. Although he's been officially off work for a month he has been exploring the tunnels beneath the Institute for two weeks on two different expeditions.
As Martin is no longer living in the Archives, he was able to get the key from Elias' desk and get into the trap door one night. Equipped with a torch, he descended into the trap door and down the steps. Underneath he found that the corridors were all different shapes and sized, but winded around unpredictably and organically.
After half an hour of exploring he found found dead worms, with a clear line between worms filled and worm free corridors. After an hour of searching he grew concerned that his torch might run out of power and decided to turn back. On the way he found several doors, including the one to the room with the worms in a circle on the wall that Tim mentioned. The circle was 10 meters in diameter and the stone within seemed warped and wavey, as though it was liquid before solidifying back into rock. There was a channel through the worm corpses on the floor, suggesting someone else had been in the room. He surfaced at 3am.
After a week's worth of recovering, Jonathan ventured into the tunnels again, ready with 3 torches, a day's worth of batteries, food and water, white chalk, a large knife and a CO2 canister from the Archives. As he explored, he marked an arrow on the walls pointing the way he had come. Within half an hour he was further than last time, into where Milbank Prison had stood.
Jonathan reflected on Milbank Prison: saying it was started in 1799, but passed through various designers before ending with Robert Smirk finishing it in 1821 [the case suggests that the prison was completed in 1815, but the actual real life one was completed in 1821].
Eventually he found a set of stairs which went up into a stone wall, and further down. He decided that he would explore all of the first level before he continued downwards, but soon found another staircase with an arrow pointing downwards. Following it, he came into a straight angled corridor and heard soft footsteps up ahead. Four levels down, he found an old wine bottle from 2003. After drawing an arrow on the wall he looked up to see the turn at the end of the corridor had disappeared. He turned around and found the way he had come had gone. Stepping back in astonishment he bumped into the wall behind him, realising that the walls were closing in on him without seeming to move. After a few minutes he heard a single word from the darkness: "leave". He did and returned to the Archives.
Jonathan doesn't care too much about the tunnels, but really wants to discover the cause of Gertrude's fate. He believes it's someone at the Archives. Elias is the most likely person, but any of his colleagues could have done it. He is going to make supplemental recordings on his spare tape recorder and will hide the tapes whilst he investigates what's happening at the core of the Archives.