Some Narrative Elements.

This story seems to be based around the conflict between Phillip Morton, (Antagonist) and Peter Brownrigg (Protagonist), as well as a vague impending conflict between Britain and the Spanish Armada.

In my opinion, the climax of this story is the point where Peter learns of the plot to assassinate the Queen, because I think at this point, he realizes just how important he is, as opposed to how important he thought he was. 

I think the way the setting wove back and forth over an entire country added to the sense of confusion that Peter is facing throughout the story, and makes it seem that much more chaotic. 

A little about the plot: I think the whole thing started when Peter threw the rock, because it seems like that is what threw Sir Phillip's hunt into full swing. If he hadn't thrown the rock, he would never have had to leave to town, and he would've carried on with a normal life. After that, I think everything up to the point where he learns of the plot to kill the Queen could be considered the rising action, and everything after that, including the capture and escape of Peter and the confrontation with Sir Phillip can be seen as the falling action.