Thomas Phelippes was the perfect Elizabethan spy. A brilliant cryptyanalyst, a skilled and intuitive handler of secret agents, and someone well used to serving powerful men in government, he might have ended his career as a senior official in the royal administration. He died instead in poverty after serving long terms of imprisonment. Early promise and promotion, a decade of clinging on to favour, half a lifetime of disgrace: this was the career trajectory of the most secret man in Elizabeth I’s government.

Born around 1556, Phelippes was the eldest son of Joan and William Phelippes, a London cloth merchant and customs officer with a house on Leadenhall Street in the City, an esquire with a coat of arms and property in Suffolk and London. He was most likely educated at the University of Cambridge, where a ‘Thomas Philips’ (the surname varies in spelling in the sources) of Trinity College graduated bachelor of arts in the academic year 1573/74 and master of arts in March 1577. Cambridge may help to explain why, by June 1578, Phelippes was employed in the household of Sir Francis Walsingham, Queen Elizabeth’s principal secretary, who himself had studied in the university. The supposition of a Trinity connection for Phelippes is further strengthened by his friendship with the lawyer, essayist and polymath Francis Bacon, younger than Phelippes by about five years, who was a student in the college between 1573 and 1575.

The ‘young Phelippes’, who was sent by Secretary Walsingham to Elizabeth’s ambassador in Paris in June 1578, was a talented linguist, fluent in French, Spanish and Latin and probably Italian and Flemish, too. He was also a mathematician and a brilliant codebreaker. ‘Phelippes the decipherer’ is a familiar phrase in Walsingham’s correspondence in the early 1580s. He worked in and around Paris between 1578 and 1583, acting in a support role to the English embassy in the ambassador’s house on the Seine near the cathedral of Notre Dame. He decrypted and translated letters sent to Philip II of Spain by his ambassador to the French court – perhaps Phelippes engineered their interception, either by theft or by suborning the couriers who carried them. In 1582 and 1583 he was posted to Bourges and Sancerre on French missions he was too discreet to describe in letters to Walsingham. His confidence in Sir Francis, and Walsingham’s in him, was expressed by Phelippes in one letter to his master in March 1582, not quite explaining why he hadn’t communicated for a few weeks: ‘Assuring myself of your honour’s gracious interpretation of all mine actions, I persuade myself it shall be needless for to use many words in the way of excuse.’

In the years following his stay in France, Phelippes was busy in London working for Walsingham as his master’s chief intelligence officer, running spies at home and abroad and summarising and processing for Sir Francis their secret reports. His mindset was one of danger and conspiracy, where enemies abroad all conspired to destabilise Protestant England by plotting Elizabeth’s murder and planning the invasions of England and Ireland: these enemies were Catholic Spain in particular, the Catholic nobility in France, the Pope, Jesuits and other Catholic priests, and Mary Queen of Scots and her supporters. The Queen of Scots, a blood relation of Elizabeth through their shared descent from the Tudor king Henry VII, as well as being a daughter of the ultra-Catholic Guise family of France, was touted by some Catholics as the rightful monarch of England and Ireland. Elizabeth’s ministers had long viewed Mary as the greatest threat to Elizabeth’s crown. Since 1568, as a refugee monarch deposed from the throne of Scotland, she had been Elizabeth’s unwanted guest in England, kept under close guard in secure locations in the midlands.

Phelippes was never busier than in the years between 1584 and 1586, the high point of anxiety over the Queen of Scots, of fears of invasion planned by Spain, France and the Pope, and of plots to assassinate Elizabeth. The spies sent to France by Walsingham and Phelippes in 1584 got close to Mary’s associates in Paris and, by 1585, Phelippes began to see clearly that he might be able to control the flow of the secret letters passing to and from Mary in England and her supporters across Catholic Europe. Getting his agents close to one group of her sympathisers in London, who were led at first by a priest named John Ballard before falling under the influence of a Derbyshire gentleman called Anthony Babington, Phelippes monitored and steered a plot whose purposes were to free the Scottish queen from prison and apparently to murder Elizabeth. By the summer of 1586 Phelippes was running the postal system that ran between Babington and the Queen of Scots, and he himself travelled to Chartley in Staffordshire to be as close as he could to Mary and her household. For weeks he tirelessly intercepted, read and copied her letters, all with the knowledge of Mary’s gaoler at Chartley, Sir Amias Paulet, and keeping Secretary Walsingham closely briefed.

It was a brilliant and ruthless intelligence operation, which demonstrated Phelippes’s superlative skills. He knew Babington’s code and cipher system better than Babington did, and in one letter Phelippes forged a postscript supposedly added by the Scottish queen in which she asked for even more specific information about the planned assassination of Elizabeth (her undoctored original demonstrated that she knew something about it already). Babington responded, and it was enough: within days his network of gentleman conspirators, who had been watched for weeks by Phelippes’s men, was rolled up, and Elizabeth’s ministers set to work to prosecute the Queen of Scots for treason against her cousin. In September 1586 Phelippes gathered the evidence and paperwork for Mary’s trial, briefing Elizabeth; he knew the material better than anyone else. In October at Fotheringhay Castle in Northamptonshire and Star Chamber at Westminster a special commission heard the evidence against the Scottish queen. They found her guilty and, after months of hesitation by Elizabeth, she was beheaded at Fotheringhay in February 1587. None of this would have happened without Thomas Phelippes.

Everything changed for Phelippes when Sir Francis Walsingham died in April 1590. Phelippes was not a civil servant in a government department; there was no Elizabethan secret service. He was his master’s servant at a royal court dominated by the patronage ambitions of ministers, and without a patron in 1590 and 1591 Phelippes was left unanchored – the spies he still employed he paid out of his own pocket. Months after Walsingham’s death, Phelippes’s father William also died, leaving his eldest son a signet ring, a library of books and the reversion of his job in the London customs house. But Phelippes needed a patron, and it was through his friend Francis Bacon that in 1592 he was recruited into the service of the rising star of Elizabeth’s court, Robert Devereux, 2nd earl of Essex, a favourite of the queen though not yet a member of her Privy Council. Essex hoped to impress Elizabeth into giving him a ministerial promotion by staging a brilliant espionage operation against English dissident Catholics in France and the Netherlands. Phelippes, so skilled at infiltrating the emigres, was the man he chose to run it.

We might say that 1592 was the watershed year of Thomas Phelippes’s career. In the 1580s he had been brilliant and dangerous. In the 1590s he struggled, and his situation only got worse. Phelippes wasn’t able to pull off a spectacular espionage coup in the Low Countries, and Essex quickly lost patience with him. By 1593 he found himself trapped between the earl’s antipathy and the suspicions of Essex’s rivals, the Cecils: William Cecil, Lord Burghley (Elizabeth’s most powerful minister); and Burghley’s son, Sir Robert Cecil. In December 1594 an audit of the London customs house revealed that Phelippes was unable to pay into the queen’s Exchequer 14 months’ worth of the revenue he had collected. The sum was a staggering £10,000 (enough to pay for an Elizabethan field army on a few months’ active service), which Phelippes may have put into moneylending, trying to turn a profit before the Exchequer payment was due. Elizabeth never forgave him, and Lord Treasurer Burghley was furious. The debt and the disgrace hung over him for the rest of his life. For so skilled, clever and intuitive a man, it was an extraordinary miscalculation. By 1597 the land and estates he had been granted in happier times had been taken from him, his house in Whittington College near the Thames was stripped of furniture, and his long-suffering wife Mary was desperately trying to agree terms with her husband’s creditors.

Though Lord Burghley had used Phelippes in the late 1590s to decipher secret communications, the Cecils never really trusted him, but there was enough of a thaw in their relationship by spring 1600 for Phelippes to offer his services to Sir Robert Cecil, by then principal secretary. Cecil accepted, and for a few years Phelippes wrote regular intelligence digests for him on news from France, the Netherlands and further afield in Europe. Phelippes was the most assiduous employee, desperate to prove himself, but his situation was always fragile; in the unforgiving world of Elizabethan court politics, Phelippes was only secure so long as he was useful. He felt favour slip away on Elizabeth’s death in 1603. Her successor, James VI of Scotland, now James I of England, son of Mary Queen of Scots, knew that Phelippes had been the primary instrument of his mother’s execution.

The final collapse of Thomas Phelippes’s career happened in 1604 and 1605. The kind of espionage operation that had worked so effectively for him in the 1580s, where he infiltrated his own agents into foreign dissident groups, feeding them with false information, could only work when he was fully trusted and supported by Secretary Walsingham. In 1605, when it was revealed to Sir Robert Cecil that Phelippes had been corresponding with the gunpowder conspirators’ foreign supporters in Catholic Brussels without Cecil’s knowledge and permission, Phelippes was sent first to the Gatehouse prison in London and then to the Tower. After that he was rarely out of prison, either for political reasons or for the debt to the Crown he could never pay off. He frequently but vainly petitioned Robert Cecil for help until Cecil’s death in 1612. Impoverished, and beset by failing eyesight, in 1625 Phelippes wrote from his ‘doghole’ in prison ‘without comfort or means to relieve myself and those that depend upon me’. By March 1626 he was dead.

Near Chartley in 1586 Mary Queen of Scots had seen from a distance a young man she thought might be an ally working secretly on her behalf: he was about 30 years of age, short and slight of build, with blonde hair and beard, and a faced scarred by smallpox. He was Thomas Phelippes, the closest template we have from the 16th century to a modern professional intelligence officer, a man who prided himself on his mastery of espionage technique and was proud of what secrets he could draw out from an enemy. As he wrote to Sir Robert Cecil in 1600: ‘I will be glad and vow unto you to employ that dexterity I may have to the utmost of my power.’