Thomas Phelippes, the son of a cloth merchant, was born in 1556. It is believed he entered Trinity College, Cambridge, in 1569 and graduated BA in 1574. (1) Phelippes was a linguist who could speak French, Italian, Spanish, Latin and German. He was described at the time as a man "of low stature, slender every way, dark yellow haired on the head, and clear yellow beared, eaten in the face with smallpox, of short sight, thirty years of age by appearance." (2)
In 1573 Francis Walsingham became Principal Secretary to Queen Elizabeth. Walsingham was given government money to setup Britain's first counter-intelligence network. Walsingham was given responsible for the security of the monarch. To protect Elizabeth he created a network of spies in Europe. He received regular reports from twelve locations in France, nine in Germany, four in Italy, four in Spain, and three others in Europe.
To keep his network running smoothly, Walsingham established a spy-school in his own London house. His school taught cipher and forgery and gave potential agents training in field-work. During this period he recruited Thomas Phelippes. He soon became Walsingham's assistant, and England's first great cryptanalyst. (3) According to his biographer, William Richardson: "His expertise was varied - as cryptographer, forger, and gatherer of secret correspondence." (4)
In March 1586, Anthony Babington and six friends gathered in The Plough, an inn outside Temple Bar, where they discussed the possibility of freeing Mary, assassinating Elizabeth, and inciting a rebellion supported by an invasion from abroad. With his spy network, it was not long before Walsingham discovered the existence of the Babington Plot. To make sure he obtained a conviction he arranged for Gifford to visit Babington on 6th July. Gifford told Babington that he had heard about the plot from Thomas Morgan in France and was willing to arrange for him to send messages to Mary via his brewer friend. (5)
However, Babington did not fully trust Gifford and enciphered his letter. Babington used a very complex cipher that consisted of 23 symbols that were to be substituted for the letters of the alphabet (excluding j. v and w), along with 35 symbols representing words or phrases. In addition, there were four nulls and a sybol which signified that the next symbol represents a double letter. It would seem that the French Embassy had already arranged for Mary to receive a copy of the necessary codebook. (6)
Gilbert Gifford took the sealed letter to Francis Walsingham. He employed counterfeiters, who would then break the seal on the letter, make a copy, and then reseal the original letter with an identical stamp before handing it back to Gifford. The apparently untouched letter could then be delivered to Mary or her correspondents, who remained oblivious to what was going on. (7)
The copy was then taken to Thomas Phelippes. "In the ciphers used by Mary and her correspondents the letters of each word were encrypted using a system of substitutes or symbols which required for their decoding the construction of a parallel alphabet of letters. To establish such cipher keys Phelippes employed frequency analysis in which individual letters were identified in the order of those most commonly used in English and the less frequent substitutes deduced in the manner of a modern crossword puzzle." (8) Eventually he was able to break the code used by Babington. The message clearly proposed the assassination of Elizabeth.
Walsingham now had the information needed to arrest Babington. However, his main target was Mary Queen of Scots and he therefore allowed the conspiracy to continue. On 17th July she replied to Babington. The message was passed to Phelippes. As he had already broken the code he had little difficulty in translating the message that gave her approval to the assassination of Elizabeth. Mary Queen of Scots wrote: "When all is ready, the six gentlemen must be set to work, and you will provide that on their design being accomplished, I may be myself rescued from this place." (9)
Walsingham now had enough evidence to arrest Mary and Babington. However, to destroy the conspiracy completely, he needed the names of all those involved. He ordered Phelippes to forge a postscript to Mary's letter, which would entice Babington to name the other men involved in the plot. "I would be glad to know the names and qualities of the six gentleman which are to accomplish the designment; for it may be that I shall be able, upon knowledge of the parties, to give you some further advice necessary to be followed therein, as also from time to time particularly how you proceed."
Simon Singh, the author of The Code Book: The Secret History of Codes & Code-Breaking (2000) has pointed out: "The cipher of Mary Queen of Scots clearly demonstrates that a weak encryption can be worse than no encryption at all. Both Mary and Babington wrote explicitly about their intentions because they believed that their communications were secure, whereas if they had been communicating openly they would have referred to their plan in a more discreet manner. Furthermore, their faith in their cipher made them particularly vulnerable to accepting Phelippes's forgery. Sender and receiver often have such confidence in the strength of their cipher that they consider it impossible for the enemy to mimic the cipher and insert forged text. The correct use of a strong cipher is a clear boon to sender and receiver, but the misuse of a weak cipher can generate a very false sense of security." (10)
Walsingham allowed the letters to continue to be sent because he wanted to discover who else was involved in this plot to overthrow Elizabeth. Eventually, on 25th June 1586, Mary wrote a letter to Anthony Babington. In his reply, Babington told Mary that he and a group of six friends were planning to murder Elizabeth. Babington discovered that Walsingham was aware of the plot and went into hiding. He hid with some companions in St John's Wood, but was eventually caught at the house of the Jerome Bellamy family in Harrow. (11) On hearing the news of his arrest the government of the city put on a show of public loyalty, witnessing "her public joy by ringing of bells, making of bonfires, and singing of psalms". (12)
Babington home was searched for documents that would provide evidence against him. When interviewed, Babington, who was not tortured, made a confession in which he admitted that Mary had written a letter supporting the plot. At his trial, Babington and his twelve confederates were found guilty and sentenced to hanging and quartering. "The horrors of semi-strangulation and of being split open alive for the heart and intestines to be wrenched out were regarded, like those of being burned to death, as awful but in the accepted order of things." (13)
Gallows were set up near St Giles-in-the-Field and the first seven conspirators, led by Babington, were executed on 20th September 1586. Babington's last words were “Spare me Lord Jesus”. Another conspirator, Chidiock Tichborne, made a long speech where he blamed Babington "for drawing him in". (14) The men "were hanged only for a short time, cut down while they were still alive, and then castrated and disembowelled".
The other seven were brought to the scaffold the next day and suffered the same death, "but, more favourably, by the Queens commandment, who detested the former cruelty" They hung until they were dead and only then suffered the barbarity of castration and disembowelling. The last to suffer was Jerome Bellamy, who was found guilty of hiding Babington and the others at his family's house in Harrow. His brother cheated the hangman by killing himself in prison. (15)
Thomas Phelippes became the most important figure in Walsingham network. According to his biographer, William Richardson: "By 1586 Phelippes had married his wife, Mary. It seems there were no children, and throughout their married life Mary supported and assisted her husband in his work. For the next four years he was the linchpin in Walsingham's extensive intelligence service: paying agents; drafting copious memoranda and dispatches; collecting examples of codes and alphabets; maintaining an extensive correspondence with agents in Scotland, France, and the Netherlands; deciphering and encrypting secret correspondence; and handling letters intercepted by the government." (16)
When Sir Francis Walsingham died in April 1590, he was employed by Robert Devereux, Earl of Essex, took command of the intelligence service. (17) Essex was now able to provide secret information direct to Queen Elizabeth. "The queen appreciated the quality of the information she received. Intelligence lay at the very heart of her policy, so she welcomed the fact that, thanks to Essex, she learned things that not even the Cecils knew. One of the secrets of her authority was an ability to boast of being the best-informed person in her realm. She could not, therefore, depend on a single source and was quite happy to encourage competition in this sphere." (18)
It is claimed that Roderigo Lopez incurred the hostility of Essex, when he revealed that he had treated him for syphilis. (19) Essex asked Phelippes to investigate Lopez. He discovered a secret correspondence between Estevão Ferreira da Gama, and the count of Fuentes, in the Spanish Netherlands. This was followed by the arrest of Lopez's courier, Gomez d'Avila. When he was interrogated he implicated Lopez. Phelippes also discovered a letter that stated: "The King of Spain had gotten three Portuguese to kill her Majesty and three more to kill the King of France". (20)
On 28th January 1594, Essex, wrote a letter to Anthony Bacon: "I have discovered a most dangerous and desperate treason. The point of conspiracy was her Majesty's death. The executioner should have been Doctor Lopez. The manner by poison. This I have so followed that I will make it appear as clear as the noon day." (21)
William Cecil was put in a difficult situation as he was employing Lopez, along with Portuguese-Jewish called Manuel de Andrada, as double-agents. To protect his sources, Cecil told Queen Elizabeth that there was no evidence against Lopez. Elizabeth told Essex that she considered the "evidence as a tissue of malicious fabrications" and Essex as a "rash and temerarious youth". (22)
According to Lacey Baldwin Smith, the author of Treason in Tudor England (2006): "Enraged and humiliated, the Earl stalked out of the royal presence, dashed at breakneck speed back to London and Essex House, and locked himself into his private bedchamber. For two days, oscillating between bouts of obsessive brooding and overwork, Essex examined, cross-examined, and re-examined everyone concerned with Lopez." (23)
Essex arranged for Manuel Luis Tinoco, and Estevão Ferreira da Gama to be tortured. They confessed that they had indeed been involved in a conspiracy with Roderigo Lopez to murder Queen Elizabeth. (24) They claimed they had agreed to poison the Queen for 50,000 crowns paid by Philip II. On the rack, he confessed that he had accepted money from the Spanish intelligence services to carry out the poisoning using exotic drugs he had obtained abroad. (25) Worn down by relentless interrogation, "Lopez agreed to all manner of improbable plots, signed his confession and so sealed his fate." (26) It has been argued that Essex was exploiting the "anti-Semitic atmosphere" of Tudor England. (27)
Sir Edward Coke, the Attorney-General, opened the trial by arguing that the three men had been seduced by Jesuit priests with great rewards to kill the Queen "being persuaded that it is glorious and meritorious, and that if they die in the action, they will inherit heaven and be canonised as saints". He pointed out that Lopez was "her Majesty's sworn servant, graced and advanced with many princely favours, used in special places of credit, permitted often access to her person, and so not suspected... This Lopez, a perjuring murdering traitor and Jewish doctor, more than Judas himself, undertook the poisoning, which was a plot more wicked, dangerous and detestable than all the former." (28)
Coke emphasized the three men's secret Judaism and they were all convicted of high treason and sentenced to be hanged, drawn, and quartered. (29) However, the Queen remained doubtful of her doctor's guilt and delayed giving the approval needed to carry out the death sentences. William Cecil wanted to ensure that Lopez was executed to protect himself from a possible investigation. "From Cecil's point of view Lopez knew too much and therefore had to be silenced". (30)
Roderigo Lopez, Manuel Luis Tinoco, and Estevão Ferreira da Gama were executed at Tyburn on 7th June 1594, without Elizabeth ever having signed a death warrant. (31) Elizabeth allowed his widow Sarah Lopez to retain the whole of her late husband's estate. This was a sign that she was still not convinced that Lopez was really involved in a plot against her. (32)
Phelippes's lost his regular income after the Roderigo Lopez case. His employment in intelligence was sporadic. In 1595 he was imprisoned in the Marshalsea and then in the Fleet as a debtor. It is estimated that he owed £11,683. Even in prison he was sometimes sent coded letters to decipher by William Cecil. He was released in June 1597, and was retained by Robert Cecil as his personal intelligencer.
The death of Queen Elizabeth and the accession of James I meant he was stripped of his pension. In January 1605 he was again imprisoned for debt. Released after ten weeks, Phelippes resumed intelligence duties and was involved in apprehending the conspirators in the Gunpowder Plot. However, in January 1606 Guy Fawkes claimed that close friends of Phelippes were involved in the plot. Phelippes was imprisoned in the Tower of London for over four years. It is believed he died in around 1625. (33)
To keep his network running smoothly, Walsingham established a spy-school. He used his own London house and when government funds proved inadequate, his own money, as the penny-pinching Elizabeth, on whose behalf all the effort was expended, was too mean to use her own. His school taught cipher and forgery and gave potential agents a thorough grounding in field-work. The most proficient graduate of the cipher school was Thomas Phelippes, soon to become Walsingham's assistant, and England's first great cryptanalyst.
Upon receiving any message to or from Mary, Phelippes devoured it. He was a master of frequency analysis, and it would be merely a matter of time before he found a solution. He established the frequency of each character, and tentatively proposed values for those that appeared most often. When a particular approach hinted at absurdity, he would backtrack and try alternative substitutions. Gradually he would identify the nulls, the cryptographic red herrings, and put them to one side. Eventually all that remained were the handful of codewords, whose meaning could be guessed from the context.
When Phelippes deciphered Babington's message to Mary, which clearly proposed the assassination of Elizabeth, he immediately forwarded the damning text to his master. At this point Walsingham could have pounced on Babington, but he wanted more than the execution of a handful of rebels. He bided his time in the hope that Mary would reply and authorise the plot, thereby incriminating herself. Walsingham had long wished for the death of Mary Queen of Scots, but he was aware of Elizabeth's reluctance to execute her cousin. However, if he could prove that Mary was endorsing an attempt on the life of Elizabeth, then surely his queen would permit the execution of her Catholic rival.