Dangerous cipher that led to the death of a queen

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IT HAS all the elements of a best-seller – a Scots-born, French-speaking queen, held prisoner by her powerful English cousin, becomes entangled in a secret plot to dethrone her captor. In her despair she communicates with her supporters with a series of letters written in an elaborate, encrypted code.

Truth can of course be stranger than fiction and history reveals that this is exactly what unfolded in the last days of the tragic life of Mary, Queen of Scots, executed in 1587 on the orders of her cousin, Queen Elizabeth I of England.

Mary had thrown herself on the mercy of the English queen after she was forced to abdicate the Scottish throne in favour of her baby son, James, in 1567. But after an inquiry held that she had plotted with her third husband, the Earl of Bothwell, to murder her second husband, Lord Darnley, Mary became Elizabeth's long-term prisoner.It was not a situation Mary and her supporters were willing to endure. Between 1571 and 1586, numerous plots were hatched to free Catholic Mary and put her in Protestant Elizabeth's place. While Elizabeth was aware that Mary's religious-based support was a continuing threat to her very existence, and strongly suspected there were plots against her, she was reluctant to accuse her own cousin of treason without proof. Events would give Elizabeth the evidence she needed to act.

In July 1586 Mary was a prisoner under the guard of a staunch Protestant, Sir Amias Paulet, at Chartley Castle in Staffordshire when she received a letter from Sir Anthony Babington, asking for her to approve "the dispatch of the usurping Competitor" – in other words, the assassination of Elizabeth.

Mary had her letters encrypted by her cipher secretary, Gilbert Curle, and then smuggled out of Chartley in casks of ale. The secret code substituted symbols for letters of the alphabet and also some words. The cipher also included some "nulls", or symbols which represented nothing at all, to confuse anyone trying to decipher the letters.

Unfortunately for Mary, the courier was a Catholic double-agent, Gilbert Gifford, who was also working for Elizabeth's principal secretary and head of intelligence, Sir Francis Walsingham. Everything she wrote was being intercepted and her reply to Babington was passed to Walsingham's master codebreaker, Sir Thomas Phelippes, a Cambridge-educated language specialist.Phelippes, who was fluent in six languages, used a technique known as frequency analysis to work out how to break the code. He started by looking for the symbols used to denote the most commonly used letters of the alphabet – "e" and "a" – and worked from there.

Mary's encryption was not only deciphered, her letter to Babington was also amended; Phelippes shrewdly added a postscript, asking Babington for the names of others involved in the plot. The conspirators were rounded up and executed.

The letters – many of which have survived and are held by the National Archives in London – were used as incontrovertible proof that Mary was actively plotting to remove Elizabeth from the throne. Mary wrote: "Orders must be given that when their design has been carried out I can be ... got out of here."

In her biography, Mary Queen of Scots, first published in 1969, Antonia Fraser records how Elizabeth's emissary, Sir Thomas Gorges, confronted her with the evidence:

"Madame, the Queen, my mistress finds it very strange that you, contrary to the pact and engagement made between you, should have conspired against her and her State, a thing which she could not have believed had she not seen proofs of it with her own eyes and known it for certain."

Mary was taken to Fotheringay Castle and tried in October 1586. Her denials were useless against the weight of evidence against her. Elizabeth finally signed the death warrant on 1 February 1587 and a week later Mary was beheaded – the form of execution reserved for the nobility.

Fraser questions whether Mary, who she says was being held illegally, should be judged too harshly for her reply to Babington, which appeared to support his suggestion that Elizabeth should be assassinated, writing: "Her own agreement was entirely in the context of a captive seeking to escape her guards, and may be compared to the actions of a prisoner who is prepared to escape by a certain route, even if it may involve the slaying of a jailer by another hand."

If Mary's secret cipher had not been cracked, Elizabeth might well have been assassinated and a Catholic queen put on the throne of England. The course of British history could have been very different.

But perhaps Mary had the final triumph – her son, James VI of Scotland, became James I of England when Elizabeth died childless in 1603.

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