VGFacts

The real-life Edward Kelley was an alchemist who worked for the Queen during the time. However, he was arrested by the Roman Empire for failing to create gold and died in prison. The Kelley met in the game is a homunculus created by John Dee months after the original's death. In the second visit to the Tower of London, the before the boss, there are clones who have the same memorandum as the first one. 

"I am the hollowed man. I am the hollowed man. Many times I've died. Many times rose again."

Source:
https://www.youtube.com/watch?v=VJePjKRfoI8