In late 16th-century England, Queen Elizabeth was a Protestant royal who faced perpetual threats to her life and reign. Real enemies and exaggerated fears led to paranoia—and the royal court responded with a secret war.

In what would become England’s first great brush with espionage, spies and even kidnappers were deployed to keep the queen safe.

The threats facing late Tudor England came from both home and abroad. Decades of hostility between Spain and England were exacerbated by England’s provocative policy of letting privateers raid Spanish treasure fleets. As the Spanish King Philip II lost patience with his piratical neighbors, the English rightly feared invasion. In 1588, Spain dispatched a 130-ship naval fleet as part of a planned invasion of England. The Spanish Armada ultimately failed, but it fueled paranoia about Spanish intrusions.

Within England, meanwhile, Mary Queen of Scots, a rival for Elizabeth’s throne, was living under house arrest. Some Catholics hoped to overthrow Elizabeth and replace her with Mary. Catholic priests such as Edmund Campion were smuggled into England, where they preached to secret congregations. To some, they were upholders of true faith. To Elizabeth, they were secret agents stirring up treason.

Fear and anxiety riddled the English court. “It’s the same sort of thing that the U.S. went through with communism in the 1950s,” says Patrick Martin, historian and author of Elizabethan Espionage.

The first significant covert operation was the kidnapping of John Story in 1570. An English Catholic, Story had fled to the Low Countries, where he plotted against Elizabeth while working for the Spanish. Sir William Cecil, one of Elizabeth’s chief advisors, ordered agents to kidnap Story and bring him home for questioning. Cecil’s agents tricked Story into searching their boat, trapped him onboard, and whisked him away.

Another of Elizabeth’s advisors, Sir Francis Walsingham, built up an ongoing spy network. A man of incredible intelligence and cunning, Walsingham used merchants to gather intelligence from across Europe.

“Merchants were very useful in moving secret information about,” says Stephen Alford, professor of early modern British history at the University of Leeds. “Merchants and their factors and agents are used to moving around Europe relatively easily.”

Walsingham’s men infiltrated Catholic circles at home and abroad. The letters of foreign ambassadors and nobles were copied by English agents while the names and movements of English rebels were carefully gathered.

The spies had a few special tricks up their sleeves. “They practiced secret inks,” explains Alford. “Quite a lot of use of code and cypher, which to our eyes looks relatively unsophisticated, although it develops an increasing sophistication.”

Cyphers became particularly important during the infamous Babington Plot, when Walsingham’s agents decrypted letters to and from Mary Queen of Scots. This provided evidence that Mary was conspiring against Elizabeth, leading to Mary’s trial and execution.

The unravelling of the Babington plot was a dramatic success, but it was far from the only one. Several of the dreaded priest infiltrators were found by an agent named George Eliot, who had infiltrated Catholic households as a servant. These priests were arrested and put on trial.

Between 1593 and 1594, agents uncovered an alleged plot by the Queen’s own physician, Dr. Rodrigo Lopez. Lopez had been in secret contact with the Spanish court and was accused of scheming to assassinate Elizabeth. In 1588, Spain had dispatched a 130-ship naval fleet as part of a planned invasion of England. The invasion failed, but with the invasion fresh in people’s minds, it was easy to imagine that the accusations against Lopez were true. Despite Lopez’s protestations of innocence, he was executed for treason.

In addition to thwarting Catholic plots at home, the Elizabethan spy network gathered intelligence on foreign schemes. This included military and political plans, as well as the identities of Catholic agents being prepared in Rome.

Walsingham died in 1590 and since there was no structure in place to maintain the spy network, much of his work was lost. The Earl of Essex and Sir Robert Cecil both tried to take Walsingham’s place as spymaster, using their achievements to compete for position at court. But, with no single person in charge, English agents often failed to collaborate.

With time and practice, Cecil became a highly effective spymaster, running a network of agents through his secretariat. Still, the lack of cooperation between him and Essex meant that information fell through the gaps. Spies provided no advance warning of the second and third Spanish armadas, and if these fleets had not been scattered by storms then England would have been exposed to attack.

The nature of spying means that evidence for it is incomplete. Little is known about Spanish spies against England, while mystery hangs around the possible role of 16th-century playwright Christopher Marlowe. Some claim that he was a spy for the court, and that this led to his murder in 1593. But without better evidence, historians will never be sure.

England’s first great experiment in government-backed spying network brought down a queen and perhaps a playwright, saw kidnappings, executions and murders. The fact that Queen Elizabeth reigned for 44 years—and died naturally in her sleep—is evidence of its success.