The Babington plot, which was the undoing of Mary, Queen of Scots, was one of several conspiracies against Elizabeth I that were uncovered. The Ridolfi Plot In 1571 a plot was discovered involving Philip II of Spain, Pope Pius V and the Duke of Norfolk, as well as Mary's advisor, the Bishop of Ross, and Mary herself.
Very interesting article that begins with the story of Mary, Queen of Scots, and continues to speak about different techniques of encryption that are harder and harder to break. It also deals with the fact that Mary's messages were being intercepted and the article speaks about secure encryption using photons where you would know if your message was intercepted.