Born into a family of English diplomats and civic servants, Francis Throckmorton turned against the status quo represented by his family in favor of plotting to overthrow Queen Elizabeth I, restore the Catholic church in England, and place Elizabeth's cousin, Mary, Queen of Scotland, on the English throne.

There seems to have been some trouble regarding his father and his standing at court, as he was suddenly dismissed from his position as chief justice of Chester in 1580. However, as his family heritage suggests, Throckmorton was raised in a traditional English fashion, educated at Oxford and reading law at the Inner Temple in London. Like a number of English men and women at the time, he was raised to be outwardly Protestant but secretly Catholic. After he left his law studies, he traveled to the Continent, as part of a typical "Grand Tour" exploration of Europe, common to young people whose families could afford to send them on such an adventure. While there, he met some of the leading lights of the Catholic Counterreformation, mostly in Spain and France. He was convinced to join their cause, and when he returned to England in 1583, Throckmorton was armed with important communications shared between European supporters of Catholicism and their English counterparts.

He also worked as an intermediary between the imprisoned Mary, Queen of Scots and the Spanish ambassador, Bernardino de Mendoza. Naturally, Elizabeth had numerous spies looking out for anyone suspicious of providing support to Mary or those working to restore Catholicism in England. Sir Francis Walsingham, in particular, took notice of Throckmorton's activities, and a search of his house was ordered. Incriminating evidence was discovered, including lists of names of his fellow conspirators, treatises in defense of Mary, Queen of Scots, and also what was termed "infamous libels on Queen Elizabeth printed beyond seas." Throckmorton was sent to the rack for torture. He eventually admitted that he was involved in a plot to overthrow the queen and to return England to the Papal fold.

The basic plan included an invasion of England organized by Mary's relative, Henry I, Duke of Guise, which would be supported by organized groups of English Catholics, who would rise up and fight for their faith. Once Throckmorton was taken from the rack and recovered, he retracted his confession, but it was too late. He was quickly tried, convicted of high treason, and sentenced to death. He was executed in July 1584. Following quickly in his wake was the fleeing of a number of Throckmorton's co-conspirators and radical supporters of Catholicism in England. Throckmorton's arrest, trial, and execution were considered big news of the day and many with strong Catholic leanings left the country. Also, the Spanish ambassador was expelled from England, which led to the war with Spain in 1588.