The Blackthorn Key Series is by Kevin Sands. I enjoyed this series immensely. The characters were so well written. They were not overly intelligent like some kids are portrayed; they made mistakes like normal preteen kids.
Summaries of books:
Book One
The Blackthorn Key
Christopher Rowe is an orphan that is chosen to be an apothecary's apprentice. The year is 1665. His best friend is Tom, a kind and tall boy. Christopher has to solve all sorts of puzzles and clues to figure out who is murdering apothecaries in London
Book Two
Mark of the Plague
The plague has come to London along with unscrupulous men. Christopher has to figure out whether it is just the plague killing people or also evil men.
Book Three
The Assassin's Curse
Someone is attempting to kill the king's sister. Christopher is recruited to go with her to Paris and figure out who it is before they succeed.
Book Four
Call of the Wraith
On the return voyage from Paris, Christopher falls overboard and loses his memory. He struggles to figure out who he is and also who has kidnapped children in the area.
Book Five
The Traitor's Blade
There's a plot to kill the king and Christopher follows clues to figure out who is behind it.
Book Six
The Raven's Revenge
The year is now 1666. There's an underlying story line that has been building through the books of an evil mastermind that wants revenge. Can Christopher, Tom, and Sally figure out who it is and survive?
I enjoyed following along as the characters grow in wisdom and stature. I sense that the author might be catholic. There was a definite reverence for God throughout the books, though one could argue the "voice" Christopher hears in his head takes the place of the Holy Spirit. I didn't mind the voice, because you know who it is suppose to be (no spoilers). The series has a very satisfying ending. I will definitely read through these again!