The conspiracy began on religious grounds. Catholic noblemen in England wanted to remove the Protestant queen, Elizabeth, and replace her with Mary, a Catholic. While Mary was not the driving force behind this conspiracy, she would pay the ultimate price for it. Mary had used both cryptography and steganography to communicate with the conspirators by enciphering messages (cryptography) and then hiding them for transport in kegs of beer (steganography).
Unfortunately for Mary, Queen Elizabeth's principal secretary, whose name was Francis Walsingham, was also England's spymaster. Walsingham had accumulated enough evidence to put Mary on trial for treason, under accusation of plotting to assassinate Queen Elizabeth and take the English crown.
While the methods of communication used by Mary and the conspirators were inventive, they were not entirely effective. Walsingham had intercepted several of the messages and had the encryption broken, which led to the deaths of several conspirators and, ultimately, to Mary's.